Starting phenix.real_space_refine on Wed Nov 19 02:26:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mhg_9114/11_2025/6mhg_9114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mhg_9114/11_2025/6mhg_9114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mhg_9114/11_2025/6mhg_9114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mhg_9114/11_2025/6mhg_9114.map" model { file = "/net/cci-nas-00/data/ceres_data/6mhg_9114/11_2025/6mhg_9114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mhg_9114/11_2025/6mhg_9114.cif" } resolution = 3.57 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= 0.221 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 12511 2.51 5 N 3442 2.21 5 O 3912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19931 Number of models: 1 Model: "" Number of chains: 23 Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 637 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 23, 'TRANS': 66} Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "A" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "B" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "O" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "P" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "D" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "Q" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "S" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "T" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "U" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "V" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "W" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 817 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Time building chain proxies: 4.89, per 1000 atoms: 0.25 Number of scatterers: 19931 At special positions: 0 Unit cell: (134.93, 118.45, 160.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3912 8.00 N 3442 7.00 C 12511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.10 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.08 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.08 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.16 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.02 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.08 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.10 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=1.83 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.02 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.06 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " 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: 1.70 Conformation dependent library (CDL) restraints added in 949.5 milliseconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4602 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 67 sheets defined 7.6% alpha, 49.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'O' and resid 79 through 83 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'W' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.934A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.384A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.469A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.469A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.677A pdb=" N MET A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 7.276A pdb=" N CYS A 92 " --> pdb=" O TRP A 103 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TRP A 103 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG A 94 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.429A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.429A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.997A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.862A pdb=" N CYS B 92 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TRP B 103 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG B 94 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 9 through 13 removed outlier: 6.629A pdb=" N VAL O 11 " --> pdb=" O THR O 105 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 9 through 13 removed outlier: 6.629A pdb=" N VAL O 11 " --> pdb=" O THR O 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.156A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.156A pdb=" N GLY C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA C 96 " --> pdb=" O GLY C 100D" (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY C 100D" --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.634A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 9 through 13 removed outlier: 6.634A pdb=" N VAL P 11 " --> pdb=" O THR P 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.425A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET D 34 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.425A pdb=" N GLY D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA D 96 " --> pdb=" O GLY D 100D" (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY D 100D" --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.558A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 9 through 13 removed outlier: 6.558A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.243A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET F 34 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.243A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.546A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 9 through 13 removed outlier: 6.546A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 19 through 24 Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.436A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.436A pdb=" N GLY G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 9 through 13 removed outlier: 6.556A pdb=" N VAL S 11 " --> pdb=" O THR S 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA S 84 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 9 through 13 removed outlier: 6.556A pdb=" N VAL S 11 " --> pdb=" O THR S 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA S 84 " --> pdb=" O LEU S 104 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.255A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.255A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA I 96 " --> pdb=" O GLY I 100D" (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY I 100D" --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 9 through 13 removed outlier: 6.633A pdb=" N VAL T 11 " --> pdb=" O THR T 105 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN T 37 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU T 46 " --> pdb=" O GLN T 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 9 through 13 removed outlier: 6.633A pdb=" N VAL T 11 " --> pdb=" O THR T 105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 19 through 24 Processing sheet with id=AF4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.206A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.206A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP J 101 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 9 through 13 removed outlier: 6.474A pdb=" N VAL U 11 " --> pdb=" O THR U 105 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 9 through 13 removed outlier: 6.474A pdb=" N VAL U 11 " --> pdb=" O THR U 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 19 through 24 Processing sheet with id=AG1, first strand: chain 'U' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.934A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.534A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA K 96 " --> pdb=" O GLY K 100D" (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY K 100D" --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 9 through 13 removed outlier: 6.486A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 9 through 13 removed outlier: 6.486A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 19 through 24 Processing sheet with id=AG8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AG9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.701A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 10 through 12 removed outlier: 7.241A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 9 through 13 removed outlier: 6.539A pdb=" N VAL W 11 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP W 35 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS W 45 " --> pdb=" O GLN W 37 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'W' and resid 9 through 13 removed outlier: 6.539A pdb=" N VAL W 11 " --> pdb=" O THR W 105 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 19 through 24 876 hydrogen bonds defined for protein. 1851 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: 4.44 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3292 1.30 - 1.43: 6096 1.43 - 1.56: 10900 1.56 - 1.69: 62 1.69 - 1.83: 87 Bond restraints: 20437 Sorted by residual: bond pdb=" CB HIS H 35 " pdb=" CG HIS H 35 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.46e+01 bond pdb=" CB HIS K 35 " pdb=" CG HIS K 35 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.01e+01 bond pdb=" CB HIS J 35 " pdb=" CG HIS J 35 " ideal model delta sigma weight residual 1.497 1.390 0.107 1.40e-02 5.10e+03 5.84e+01 bond pdb=" CB HIS G 35 " pdb=" CG HIS G 35 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.51e+01 bond pdb=" CG GLU C 6 " pdb=" CD GLU C 6 " ideal model delta sigma weight residual 1.516 1.338 0.178 2.50e-02 1.60e+03 5.05e+01 ... (remaining 20432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 24680 2.76 - 5.51: 2799 5.51 - 8.27: 331 8.27 - 11.03: 29 11.03 - 13.79: 9 Bond angle restraints: 27848 Sorted by residual: angle pdb=" N ARG Q 61 " pdb=" CA ARG Q 61 " pdb=" C ARG Q 61 " ideal model delta sigma weight residual 114.62 100.83 13.79 1.14e+00 7.69e-01 1.46e+02 angle pdb=" N ARG S 61 " pdb=" CA ARG S 61 " pdb=" C ARG S 61 " ideal model delta sigma weight residual 114.62 102.14 12.48 1.14e+00 7.69e-01 1.20e+02 angle pdb=" N ARG V 61 " pdb=" CA ARG V 61 " pdb=" C ARG V 61 " ideal model delta sigma weight residual 114.62 102.54 12.08 1.14e+00 7.69e-01 1.12e+02 angle pdb=" N ARG R 61 " pdb=" CA ARG R 61 " pdb=" C ARG R 61 " ideal model delta sigma weight residual 114.75 101.91 12.84 1.26e+00 6.30e-01 1.04e+02 angle pdb=" N ARG P 61 " pdb=" CA ARG P 61 " pdb=" C ARG P 61 " ideal model delta sigma weight residual 114.75 102.08 12.67 1.26e+00 6.30e-01 1.01e+02 ... (remaining 27843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 11356 16.37 - 32.75: 238 32.75 - 49.12: 97 49.12 - 65.50: 70 65.50 - 81.87: 11 Dihedral angle restraints: 11772 sinusoidal: 4375 harmonic: 7397 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual 93.00 39.30 53.70 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CD ARG D 56 " pdb=" NE ARG D 56 " pdb=" CZ ARG D 56 " pdb=" NH1 ARG D 56 " ideal model delta sinusoidal sigma weight residual 0.00 -53.57 53.57 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 92 " pdb=" CB CYS M 92 " ideal model delta sinusoidal sigma weight residual 93.00 45.63 47.37 1 1.00e+01 1.00e-02 3.10e+01 ... (remaining 11769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1688 0.070 - 0.139: 893 0.139 - 0.209: 309 0.209 - 0.278: 71 0.278 - 0.348: 3 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA THR G 24 " pdb=" N THR G 24 " pdb=" C THR G 24 " pdb=" CB THR G 24 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB ILE T 48 " pdb=" CA ILE T 48 " pdb=" CG1 ILE T 48 " pdb=" CG2 ILE T 48 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA MET H 34 " pdb=" N MET H 34 " pdb=" C MET H 34 " pdb=" CB MET H 34 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2961 not shown) Planarity restraints: 3633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 56 " 0.887 9.50e-02 1.11e+02 3.97e-01 9.57e+01 pdb=" NE ARG D 56 " -0.051 2.00e-02 2.50e+03 pdb=" CZ ARG D 56 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 56 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 56 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 50 " -0.031 2.00e-02 2.50e+03 6.13e-02 3.76e+01 pdb=" C ILE F 50 " 0.106 2.00e-02 2.50e+03 pdb=" O ILE F 50 " -0.040 2.00e-02 2.50e+03 pdb=" N ILE F 51 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 31 " 0.067 2.00e-02 2.50e+03 3.74e-02 2.80e+01 pdb=" CG TYR L 31 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR L 31 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR L 31 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR L 31 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR L 31 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR L 31 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 31 " 0.059 2.00e-02 2.50e+03 ... (remaining 3630 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2510 2.72 - 3.26: 17847 3.26 - 3.81: 34285 3.81 - 4.35: 44633 4.35 - 4.90: 71950 Nonbonded interactions: 171225 Sorted by model distance: nonbonded pdb=" N ASP G 101 " pdb=" OD1 ASP G 101 " model vdw 2.175 3.120 nonbonded pdb=" N PRO E 42 " pdb=" O PRO E 42 " model vdw 2.260 2.496 nonbonded pdb=" O ILE F 51 " pdb=" O TRP F 52 " model vdw 2.264 3.040 nonbonded pdb=" OD2 ASP J 72 " pdb=" NZ LYS J 75 " model vdw 2.349 3.120 nonbonded pdb=" O ARG D 56 " pdb=" CG ASN D 57 " model vdw 2.356 3.270 ... (remaining 171220 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 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.700 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.021 0.198 20459 Z= 1.134 Angle : 1.810 13.785 27892 Z= 1.210 Chirality : 0.091 0.348 2964 Planarity : 0.012 0.397 3633 Dihedral : 9.725 81.871 7104 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.01 % Favored : 95.61 % Rotamer: Outliers : 0.24 % Allowed : 0.47 % Favored : 99.29 % 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: 0.49 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.66 (0.15), residues: 1078 loop : 0.17 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 94 TYR 0.067 0.009 TYR L 31 PHE 0.038 0.007 PHE G 67 TRP 0.049 0.008 TRP T 35 HIS 0.029 0.008 HIS U 34 Details of bonding type rmsd covalent geometry : bond 0.02078 (20437) covalent geometry : angle 1.80723 (27848) SS BOND : bond 0.05862 ( 22) SS BOND : angle 3.27544 ( 44) hydrogen bonds : bond 0.15951 ( 768) hydrogen bonds : angle 8.53647 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 731 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ASN cc_start: 0.8254 (m-40) cc_final: 0.8017 (m110) REVERT: H 98 TYR cc_start: 0.6228 (t80) cc_final: 0.5891 (t80) REVERT: H 109 VAL cc_start: 0.7008 (t) cc_final: 0.6407 (t) REVERT: L 37 GLN cc_start: 0.7585 (tt0) cc_final: 0.7368 (tm-30) REVERT: L 47 LEU cc_start: 0.8486 (tp) cc_final: 0.8270 (tp) REVERT: L 48 ILE cc_start: 0.8936 (mm) cc_final: 0.8721 (mt) REVERT: L 92 ASP cc_start: 0.7286 (t0) cc_final: 0.7065 (m-30) REVERT: A 3 GLN cc_start: 0.7771 (tt0) cc_final: 0.7442 (mp10) REVERT: A 29 PHE cc_start: 0.8555 (t80) cc_final: 0.7940 (t80) REVERT: A 86 ASP cc_start: 0.8088 (m-30) cc_final: 0.7860 (m-30) REVERT: N 21 ILE cc_start: 0.7735 (mp) cc_final: 0.7214 (mt) REVERT: N 82 ASP cc_start: 0.5906 (m-30) cc_final: 0.5595 (m-30) REVERT: N 92 ASP cc_start: 0.8042 (t0) cc_final: 0.7702 (t0) REVERT: N 95 LEU cc_start: 0.9013 (mt) cc_final: 0.8696 (mp) REVERT: N 104 LEU cc_start: 0.8384 (tp) cc_final: 0.8145 (tp) REVERT: B 34 MET cc_start: 0.9014 (mmm) cc_final: 0.8364 (mmp) REVERT: B 82 LEU cc_start: 0.8878 (mt) cc_final: 0.8239 (tp) REVERT: O 105 THR cc_start: 0.7621 (m) cc_final: 0.7390 (p) REVERT: C 82 LEU cc_start: 0.8904 (mp) cc_final: 0.8651 (tp) REVERT: Q 60 ASP cc_start: 0.8174 (t0) cc_final: 0.7939 (t0) REVERT: Q 105 THR cc_start: 0.7796 (m) cc_final: 0.7429 (p) REVERT: F 82 LEU cc_start: 0.9334 (mt) cc_final: 0.9108 (mt) REVERT: F 101 ASP cc_start: 0.8718 (p0) cc_final: 0.8515 (p0) REVERT: R 105 THR cc_start: 0.8458 (m) cc_final: 0.7880 (p) REVERT: G 64 GLU cc_start: 0.7893 (tt0) cc_final: 0.7608 (tt0) REVERT: S 106 LEU cc_start: 0.8046 (mt) cc_final: 0.7769 (tt) REVERT: I 69 ILE cc_start: 0.9194 (tt) cc_final: 0.8990 (tp) REVERT: T 79 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7487 (mt0) REVERT: J 108 LEU cc_start: 0.7905 (tp) cc_final: 0.7614 (tt) REVERT: U 78 LEU cc_start: 0.8865 (tp) cc_final: 0.8590 (tt) REVERT: K 56 ARG cc_start: 0.8737 (mmt-90) cc_final: 0.8525 (tpp80) REVERT: K 100 THR cc_start: 0.8657 (p) cc_final: 0.8404 (p) REVERT: V 5 THR cc_start: 0.7920 (m) cc_final: 0.7696 (p) outliers start: 5 outliers final: 4 residues processed: 735 average time/residue: 0.1721 time to fit residues: 184.0292 Evaluate side-chains 424 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 420 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 56 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 89 GLN F 73 ASN ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** S 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 ASN J 105 GLN U 53 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.065735 restraints weight = 47872.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.068319 restraints weight = 23345.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069929 restraints weight = 15513.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.071044 restraints weight = 12113.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.071634 restraints weight = 10443.968| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 20459 Z= 0.222 Angle : 0.771 10.003 27892 Z= 0.416 Chirality : 0.049 0.233 2964 Planarity : 0.005 0.058 3633 Dihedral : 5.447 57.897 2941 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 2.71 % Allowed : 11.87 % Favored : 85.42 % 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: 0.30 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.66 (0.15), residues: 1056 loop : -0.06 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.025 0.002 TYR H 100C PHE 0.027 0.003 PHE L 62 TRP 0.022 0.002 TRP F 103 HIS 0.005 0.001 HIS V 34 Details of bonding type rmsd covalent geometry : bond 0.00500 (20437) covalent geometry : angle 0.76935 (27848) SS BOND : bond 0.01005 ( 22) SS BOND : angle 1.54580 ( 44) hydrogen bonds : bond 0.04412 ( 768) hydrogen bonds : angle 6.58628 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 496 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.6975 (ttp80) cc_final: 0.6467 (ttp80) REVERT: H 37 VAL cc_start: 0.9006 (t) cc_final: 0.8630 (p) REVERT: H 90 TYR cc_start: 0.6893 (m-80) cc_final: 0.6669 (m-80) REVERT: H 100 TYR cc_start: 0.8299 (p90) cc_final: 0.7559 (p90) REVERT: H 109 VAL cc_start: 0.7610 (t) cc_final: 0.7307 (t) REVERT: L 36 TYR cc_start: 0.7023 (m-80) cc_final: 0.5850 (m-80) REVERT: L 47 LEU cc_start: 0.8197 (tp) cc_final: 0.7882 (tp) REVERT: L 86 TYR cc_start: 0.7349 (m-80) cc_final: 0.6999 (m-80) REVERT: L 92 ASP cc_start: 0.7826 (t0) cc_final: 0.7393 (t0) REVERT: A 3 GLN cc_start: 0.7817 (tt0) cc_final: 0.7407 (mp10) REVERT: A 32 TYR cc_start: 0.8365 (m-80) cc_final: 0.7654 (m-10) REVERT: A 72 ASP cc_start: 0.6976 (t0) cc_final: 0.6629 (t0) REVERT: N 21 ILE cc_start: 0.7875 (mp) cc_final: 0.7547 (mt) REVERT: N 92 ASP cc_start: 0.8483 (t0) cc_final: 0.8148 (t0) REVERT: B 102 TYR cc_start: 0.8788 (m-80) cc_final: 0.8472 (m-10) REVERT: O 83 GLU cc_start: 0.8052 (tp30) cc_final: 0.7354 (pm20) REVERT: O 92 ASP cc_start: 0.8785 (t0) cc_final: 0.8400 (t70) REVERT: C 56 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7806 (mmt-90) REVERT: C 82 LEU cc_start: 0.9213 (mp) cc_final: 0.8940 (mt) REVERT: C 105 GLN cc_start: 0.8065 (pm20) cc_final: 0.7839 (pp30) REVERT: Q 82 ASP cc_start: 0.7589 (m-30) cc_final: 0.7291 (m-30) REVERT: Q 83 GLU cc_start: 0.8351 (pm20) cc_final: 0.8031 (pm20) REVERT: R 5 THR cc_start: 0.9044 (m) cc_final: 0.8751 (p) REVERT: G 43 LYS cc_start: 0.9194 (mmtm) cc_final: 0.8992 (mmtm) REVERT: G 72 ASP cc_start: 0.7724 (t0) cc_final: 0.7445 (t0) REVERT: G 75 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8717 (mtpp) REVERT: S 103 LYS cc_start: 0.8637 (tptp) cc_final: 0.8434 (tptp) REVERT: S 106 LEU cc_start: 0.8215 (mt) cc_final: 0.7773 (tt) REVERT: T 69 THR cc_start: 0.8576 (p) cc_final: 0.8069 (t) REVERT: J 18 LEU cc_start: 0.8980 (tp) cc_final: 0.8655 (mt) REVERT: J 105 GLN cc_start: 0.8562 (mm110) cc_final: 0.8180 (pm20) REVERT: U 6 GLN cc_start: 0.8048 (mt0) cc_final: 0.7625 (mt0) REVERT: U 35 TRP cc_start: 0.8720 (m-90) cc_final: 0.8335 (m100) REVERT: U 36 TYR cc_start: 0.8999 (m-80) cc_final: 0.8737 (m-80) REVERT: U 60 ASP cc_start: 0.8478 (t0) cc_final: 0.8236 (t0) REVERT: U 103 LYS cc_start: 0.9023 (tptm) cc_final: 0.8740 (tppt) REVERT: K 56 ARG cc_start: 0.7885 (mmt-90) cc_final: 0.7369 (mmm-85) REVERT: K 82 MET cc_start: 0.7423 (mtm) cc_final: 0.7176 (mtt) REVERT: K 99 ASP cc_start: 0.9137 (t0) cc_final: 0.8907 (t70) REVERT: V 5 THR cc_start: 0.8132 (m) cc_final: 0.7758 (p) REVERT: V 79 GLN cc_start: 0.7985 (mm110) cc_final: 0.7351 (mm110) REVERT: M 29 PHE cc_start: 0.7536 (t80) cc_final: 0.7156 (t80) REVERT: M 98 TYR cc_start: 0.7921 (t80) cc_final: 0.7713 (t80) REVERT: W 34 HIS cc_start: 0.7624 (m90) cc_final: 0.6547 (m-70) REVERT: W 54 ARG cc_start: 0.6619 (ptt-90) cc_final: 0.6371 (ptt-90) outliers start: 57 outliers final: 32 residues processed: 521 average time/residue: 0.1557 time to fit residues: 122.3921 Evaluate side-chains 440 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 408 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 62 PHE Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain W residue 24 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 22 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 6 optimal weight: 0.0050 chunk 54 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN N 51 ASN N 79 GLN ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS P 34 HIS P 79 GLN Q 34 HIS R 34 HIS ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 GLN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 HIS ** U 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN V 34 HIS ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.101878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.062342 restraints weight = 48389.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.064768 restraints weight = 23660.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066390 restraints weight = 15775.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.067282 restraints weight = 12362.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.067922 restraints weight = 10730.343| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20459 Z= 0.248 Angle : 0.703 9.918 27892 Z= 0.378 Chirality : 0.046 0.189 2964 Planarity : 0.005 0.050 3633 Dihedral : 5.123 53.511 2931 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.95 % Rotamer: Outliers : 3.13 % Allowed : 12.73 % Favored : 84.14 % 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: 0.14 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.78 (0.15), residues: 1034 loop : -0.36 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 66 TYR 0.022 0.002 TYR H 52A PHE 0.020 0.003 PHE H 29 TRP 0.020 0.002 TRP J 103 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00567 (20437) covalent geometry : angle 0.70198 (27848) SS BOND : bond 0.00562 ( 22) SS BOND : angle 1.33114 ( 44) hydrogen bonds : bond 0.03918 ( 768) hydrogen bonds : angle 6.05256 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 430 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8041 (tp) cc_final: 0.7810 (mt) REVERT: H 34 MET cc_start: 0.7284 (mtp) cc_final: 0.6985 (mmt) REVERT: H 36 TRP cc_start: 0.6866 (m100) cc_final: 0.6350 (m100) REVERT: H 37 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8505 (p) REVERT: H 47 TRP cc_start: 0.7611 (t60) cc_final: 0.7233 (t60) REVERT: H 80 LEU cc_start: 0.7224 (tt) cc_final: 0.6894 (tt) REVERT: H 92 CYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6878 (m) REVERT: H 97 TYR cc_start: 0.6990 (t80) cc_final: 0.6777 (t80) REVERT: H 100 TYR cc_start: 0.8306 (p90) cc_final: 0.7705 (p90) REVERT: L 36 TYR cc_start: 0.7120 (m-80) cc_final: 0.5869 (m-80) REVERT: L 47 LEU cc_start: 0.8083 (tp) cc_final: 0.7876 (tp) REVERT: L 92 ASP cc_start: 0.7834 (t0) cc_final: 0.7304 (t0) REVERT: A 3 GLN cc_start: 0.7971 (tt0) cc_final: 0.7631 (pp30) REVERT: A 29 PHE cc_start: 0.8573 (t80) cc_final: 0.8219 (t80) REVERT: A 32 TYR cc_start: 0.8442 (m-80) cc_final: 0.7463 (m-10) REVERT: A 34 MET cc_start: 0.7629 (mmm) cc_final: 0.7156 (mmm) REVERT: A 46 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 72 ASP cc_start: 0.6661 (t0) cc_final: 0.6379 (t0) REVERT: N 21 ILE cc_start: 0.8193 (mp) cc_final: 0.7933 (mt) REVERT: N 58 VAL cc_start: 0.8891 (t) cc_final: 0.8639 (m) REVERT: N 82 ASP cc_start: 0.6644 (m-30) cc_final: 0.6123 (m-30) REVERT: N 86 TYR cc_start: 0.8108 (m-80) cc_final: 0.7851 (m-80) REVERT: N 92 ASP cc_start: 0.8532 (t0) cc_final: 0.8291 (t0) REVERT: N 104 LEU cc_start: 0.7803 (tp) cc_final: 0.7474 (tp) REVERT: B 72 ASP cc_start: 0.7977 (t0) cc_final: 0.7087 (t0) REVERT: B 75 LYS cc_start: 0.8762 (mmtm) cc_final: 0.8255 (mmtm) REVERT: B 102 TYR cc_start: 0.8728 (m-80) cc_final: 0.8414 (m-10) REVERT: O 27 ASN cc_start: 0.9064 (p0) cc_final: 0.8667 (p0) REVERT: O 92 ASP cc_start: 0.8952 (t0) cc_final: 0.8667 (t70) REVERT: C 72 ASP cc_start: 0.7879 (t0) cc_final: 0.7657 (t70) REVERT: P 69 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8373 (t) REVERT: D 43 LYS cc_start: 0.9196 (mmtp) cc_final: 0.8963 (mmmm) REVERT: F 72 ASP cc_start: 0.8283 (t0) cc_final: 0.8075 (t0) REVERT: R 5 THR cc_start: 0.9108 (m) cc_final: 0.8827 (p) REVERT: R 79 GLN cc_start: 0.8355 (mp10) cc_final: 0.7632 (mp10) REVERT: R 82 ASP cc_start: 0.8588 (m-30) cc_final: 0.8371 (m-30) REVERT: G 43 LYS cc_start: 0.9318 (mmtm) cc_final: 0.9114 (mmtm) REVERT: G 72 ASP cc_start: 0.7769 (t0) cc_final: 0.7456 (t0) REVERT: G 75 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8911 (mtpp) REVERT: S 103 LYS cc_start: 0.8670 (tptp) cc_final: 0.8350 (tptp) REVERT: S 104 LEU cc_start: 0.9146 (tp) cc_final: 0.8492 (tp) REVERT: S 106 LEU cc_start: 0.8382 (mt) cc_final: 0.7813 (tt) REVERT: I 4 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8676 (mt) REVERT: T 5 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9056 (p) REVERT: T 69 THR cc_start: 0.8643 (p) cc_final: 0.8172 (t) REVERT: J 18 LEU cc_start: 0.9045 (tp) cc_final: 0.8681 (mt) REVERT: J 72 ASP cc_start: 0.7076 (t0) cc_final: 0.6829 (t0) REVERT: J 82 MET cc_start: 0.9195 (mtm) cc_final: 0.8468 (mtm) REVERT: J 82 ASN cc_start: 0.8333 (m-40) cc_final: 0.8089 (p0) REVERT: J 99 ASP cc_start: 0.8156 (t0) cc_final: 0.7813 (m-30) REVERT: J 105 GLN cc_start: 0.8839 (mm110) cc_final: 0.8202 (pm20) REVERT: U 79 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: U 104 LEU cc_start: 0.9204 (tp) cc_final: 0.8734 (tt) REVERT: K 56 ARG cc_start: 0.8090 (mmt-90) cc_final: 0.7540 (mmm-85) REVERT: V 5 THR cc_start: 0.8239 (m) cc_final: 0.7825 (p) REVERT: M 29 PHE cc_start: 0.7640 (t80) cc_final: 0.7205 (t80) REVERT: M 36 TRP cc_start: 0.7483 (m100) cc_final: 0.7243 (m100) REVERT: W 34 HIS cc_start: 0.7454 (m90) cc_final: 0.6527 (m-70) REVERT: W 91 TYR cc_start: 0.6028 (t80) cc_final: 0.5826 (t80) outliers start: 66 outliers final: 34 residues processed: 460 average time/residue: 0.1527 time to fit residues: 106.3089 Evaluate side-chains 430 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 390 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain U residue 52 ILE Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain W residue 24 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 8 optimal weight: 20.0000 chunk 92 optimal weight: 0.0020 chunk 183 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 79 GLN Q 89 GLN T 51 ASN ** U 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.103308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.064611 restraints weight = 48077.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.067809 restraints weight = 24709.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.068704 restraints weight = 13881.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.069028 restraints weight = 13085.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.069094 restraints weight = 11568.091| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20459 Z= 0.129 Angle : 0.624 9.717 27892 Z= 0.326 Chirality : 0.044 0.162 2964 Planarity : 0.004 0.050 3633 Dihedral : 4.870 55.826 2931 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 2.71 % Allowed : 14.06 % Favored : 83.24 % 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: 0.23 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.94 (0.15), residues: 1034 loop : -0.39 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 93 TYR 0.030 0.001 TYR A 52A PHE 0.014 0.002 PHE H 29 TRP 0.014 0.001 TRP K 36 HIS 0.008 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00291 (20437) covalent geometry : angle 0.62369 (27848) SS BOND : bond 0.00390 ( 22) SS BOND : angle 0.93797 ( 44) hydrogen bonds : bond 0.03192 ( 768) hydrogen bonds : angle 5.61981 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 441 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7332 (mtp) cc_final: 0.6946 (ppp) REVERT: H 36 TRP cc_start: 0.6766 (m100) cc_final: 0.6231 (m100) REVERT: H 37 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8512 (p) REVERT: H 39 GLN cc_start: 0.5727 (tt0) cc_final: 0.5426 (tt0) REVERT: H 47 TRP cc_start: 0.7535 (t60) cc_final: 0.7104 (t60) REVERT: H 56 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7268 (mmt180) REVERT: H 92 CYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6935 (m) REVERT: H 100 TYR cc_start: 0.8183 (p90) cc_final: 0.7598 (p90) REVERT: L 35 TRP cc_start: 0.7039 (m100) cc_final: 0.6797 (m100) REVERT: L 36 TYR cc_start: 0.7172 (m-80) cc_final: 0.5830 (m-80) REVERT: L 47 LEU cc_start: 0.7977 (tp) cc_final: 0.7743 (tp) REVERT: L 49 TYR cc_start: 0.7421 (p90) cc_final: 0.7149 (p90) REVERT: L 87 TYR cc_start: 0.7026 (m-80) cc_final: 0.6812 (m-10) REVERT: L 92 ASP cc_start: 0.7670 (t0) cc_final: 0.7168 (t0) REVERT: A 3 GLN cc_start: 0.8018 (tt0) cc_final: 0.7749 (pp30) REVERT: A 29 PHE cc_start: 0.8450 (t80) cc_final: 0.8072 (t80) REVERT: A 32 TYR cc_start: 0.8359 (m-80) cc_final: 0.7401 (m-10) REVERT: A 34 MET cc_start: 0.7655 (mmm) cc_final: 0.7135 (mmm) REVERT: A 72 ASP cc_start: 0.6509 (t0) cc_final: 0.6262 (t0) REVERT: N 21 ILE cc_start: 0.8338 (mp) cc_final: 0.8109 (mt) REVERT: N 86 TYR cc_start: 0.8101 (m-80) cc_final: 0.7828 (m-80) REVERT: N 104 LEU cc_start: 0.7836 (tp) cc_final: 0.7548 (tp) REVERT: B 72 ASP cc_start: 0.7893 (t0) cc_final: 0.7021 (t0) REVERT: B 75 LYS cc_start: 0.8861 (mmtm) cc_final: 0.8332 (mmtm) REVERT: B 102 TYR cc_start: 0.8630 (m-80) cc_final: 0.8280 (m-10) REVERT: O 92 ASP cc_start: 0.8931 (t0) cc_final: 0.8683 (t70) REVERT: C 43 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8421 (mmtp) REVERT: C 82 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7903 (ptm) REVERT: P 69 THR cc_start: 0.8746 (p) cc_final: 0.8381 (t) REVERT: Q 72 SER cc_start: 0.9503 (t) cc_final: 0.9301 (p) REVERT: Q 79 GLN cc_start: 0.7784 (mp10) cc_final: 0.7532 (mp10) REVERT: Q 83 GLU cc_start: 0.8451 (pm20) cc_final: 0.8133 (pm20) REVERT: F 56 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7690 (mtp-110) REVERT: R 5 THR cc_start: 0.9112 (m) cc_final: 0.8837 (p) REVERT: R 69 THR cc_start: 0.9269 (p) cc_final: 0.8752 (t) REVERT: R 79 GLN cc_start: 0.8250 (mp10) cc_final: 0.7950 (mp10) REVERT: G 72 ASP cc_start: 0.7822 (t0) cc_final: 0.7503 (t0) REVERT: G 75 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8827 (mtpp) REVERT: S 103 LYS cc_start: 0.8605 (tptp) cc_final: 0.8220 (tptp) REVERT: S 104 LEU cc_start: 0.9209 (tp) cc_final: 0.8992 (tp) REVERT: S 106 LEU cc_start: 0.8408 (mt) cc_final: 0.7870 (tt) REVERT: T 5 THR cc_start: 0.9403 (m) cc_final: 0.9044 (p) REVERT: T 69 THR cc_start: 0.8606 (p) cc_final: 0.8183 (t) REVERT: J 18 LEU cc_start: 0.9032 (tp) cc_final: 0.8670 (mt) REVERT: J 82 MET cc_start: 0.9262 (mtm) cc_final: 0.8499 (mtm) REVERT: J 99 ASP cc_start: 0.8156 (t0) cc_final: 0.7822 (m-30) REVERT: J 105 GLN cc_start: 0.8806 (mm110) cc_final: 0.8229 (pm20) REVERT: U 69 THR cc_start: 0.8839 (p) cc_final: 0.8249 (t) REVERT: U 79 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: U 81 GLU cc_start: 0.7896 (mp0) cc_final: 0.7057 (mp0) REVERT: U 103 LYS cc_start: 0.8813 (tptp) cc_final: 0.8525 (tppt) REVERT: K 56 ARG cc_start: 0.7942 (mmt-90) cc_final: 0.7432 (mmm-85) REVERT: K 64 GLU cc_start: 0.8186 (pt0) cc_final: 0.7901 (pt0) REVERT: K 98 TYR cc_start: 0.8226 (t80) cc_final: 0.7900 (t80) REVERT: V 5 THR cc_start: 0.8290 (m) cc_final: 0.7902 (p) REVERT: V 27 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8519 (p0) REVERT: V 82 ASP cc_start: 0.8474 (m-30) cc_final: 0.8115 (m-30) REVERT: V 103 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8511 (tptt) REVERT: M 29 PHE cc_start: 0.7727 (t80) cc_final: 0.7207 (t80) REVERT: M 34 MET cc_start: 0.7315 (mmp) cc_final: 0.7105 (mmp) REVERT: M 36 TRP cc_start: 0.7487 (m100) cc_final: 0.7192 (m100) REVERT: W 34 HIS cc_start: 0.7334 (m90) cc_final: 0.6346 (m-70) REVERT: W 49 TYR cc_start: 0.7738 (p90) cc_final: 0.7414 (p90) REVERT: W 91 TYR cc_start: 0.6244 (t80) cc_final: 0.6006 (t80) outliers start: 57 outliers final: 32 residues processed: 468 average time/residue: 0.1544 time to fit residues: 109.4338 Evaluate side-chains 437 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 399 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain W residue 24 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 38 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 30.0000 chunk 179 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 11 optimal weight: 50.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 ASN ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 79 GLN T 51 ASN U 79 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.101839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.062825 restraints weight = 48521.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.065247 restraints weight = 23743.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.066847 restraints weight = 15790.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.067785 restraints weight = 12335.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.068287 restraints weight = 10659.036| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20459 Z= 0.180 Angle : 0.625 10.325 27892 Z= 0.327 Chirality : 0.044 0.176 2964 Planarity : 0.004 0.051 3633 Dihedral : 4.783 55.433 2931 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 3.18 % Allowed : 14.58 % Favored : 82.24 % 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: 0.19 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.01 (0.15), residues: 1034 loop : -0.50 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 16 TYR 0.030 0.001 TYR W 36 PHE 0.016 0.002 PHE G 67 TRP 0.016 0.001 TRP W 96 HIS 0.003 0.001 HIS W 34 Details of bonding type rmsd covalent geometry : bond 0.00416 (20437) covalent geometry : angle 0.62409 (27848) SS BOND : bond 0.00481 ( 22) SS BOND : angle 1.11051 ( 44) hydrogen bonds : bond 0.03261 ( 768) hydrogen bonds : angle 5.47326 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 412 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7276 (mtp) cc_final: 0.6893 (ppp) REVERT: H 36 TRP cc_start: 0.6912 (m100) cc_final: 0.6270 (m100) REVERT: H 37 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8521 (p) REVERT: H 39 GLN cc_start: 0.5725 (tt0) cc_final: 0.5413 (tt0) REVERT: H 47 TRP cc_start: 0.7517 (t60) cc_final: 0.7233 (t60) REVERT: H 92 CYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6740 (m) REVERT: H 100 TYR cc_start: 0.8234 (p90) cc_final: 0.7525 (p90) REVERT: L 36 TYR cc_start: 0.7108 (m-80) cc_final: 0.5961 (m-80) REVERT: L 86 TYR cc_start: 0.8120 (m-80) cc_final: 0.7173 (m-80) REVERT: L 92 ASP cc_start: 0.7746 (t0) cc_final: 0.7265 (t0) REVERT: A 3 GLN cc_start: 0.8083 (tt0) cc_final: 0.7810 (pp30) REVERT: A 32 TYR cc_start: 0.8407 (m-80) cc_final: 0.7501 (m-10) REVERT: A 34 MET cc_start: 0.7682 (mmm) cc_final: 0.7175 (mmm) REVERT: A 46 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 72 ASP cc_start: 0.6662 (t0) cc_final: 0.6347 (t0) REVERT: N 104 LEU cc_start: 0.7873 (tp) cc_final: 0.7623 (tp) REVERT: B 72 ASP cc_start: 0.7907 (t0) cc_final: 0.7006 (t0) REVERT: B 75 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8411 (mmtm) REVERT: B 102 TYR cc_start: 0.8700 (m-80) cc_final: 0.8395 (m-80) REVERT: O 92 ASP cc_start: 0.8909 (t0) cc_final: 0.8626 (t70) REVERT: P 69 THR cc_start: 0.8709 (p) cc_final: 0.8323 (t) REVERT: Q 72 SER cc_start: 0.9482 (t) cc_final: 0.9282 (p) REVERT: Q 79 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: Q 103 LYS cc_start: 0.8083 (tptm) cc_final: 0.7773 (tptt) REVERT: F 43 LYS cc_start: 0.9234 (mmtm) cc_final: 0.8991 (mmtm) REVERT: F 56 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7751 (mtp-110) REVERT: R 5 THR cc_start: 0.9119 (m) cc_final: 0.8873 (p) REVERT: R 79 GLN cc_start: 0.8343 (mp10) cc_final: 0.7571 (mp10) REVERT: G 72 ASP cc_start: 0.7761 (t0) cc_final: 0.7428 (t0) REVERT: G 75 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8797 (mtpp) REVERT: S 104 LEU cc_start: 0.9125 (tp) cc_final: 0.8771 (tp) REVERT: S 106 LEU cc_start: 0.8446 (mt) cc_final: 0.7841 (tt) REVERT: T 5 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9093 (p) REVERT: T 69 THR cc_start: 0.8655 (p) cc_final: 0.8229 (t) REVERT: J 18 LEU cc_start: 0.9021 (tp) cc_final: 0.8670 (mt) REVERT: J 82 MET cc_start: 0.9215 (mtm) cc_final: 0.8475 (mtm) REVERT: J 105 GLN cc_start: 0.8796 (mm110) cc_final: 0.8157 (pm20) REVERT: U 69 THR cc_start: 0.8858 (p) cc_final: 0.8289 (t) REVERT: U 79 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: U 81 GLU cc_start: 0.8232 (mp0) cc_final: 0.7821 (mp0) REVERT: U 87 TYR cc_start: 0.8915 (m-80) cc_final: 0.8694 (m-10) REVERT: K 56 ARG cc_start: 0.7996 (mmt-90) cc_final: 0.7501 (mmm-85) REVERT: K 64 GLU cc_start: 0.8202 (pt0) cc_final: 0.7895 (pt0) REVERT: K 82 MET cc_start: 0.7170 (mmm) cc_final: 0.6953 (mtp) REVERT: K 98 TYR cc_start: 0.8276 (t80) cc_final: 0.7966 (t80) REVERT: V 5 THR cc_start: 0.8307 (m) cc_final: 0.7961 (p) REVERT: V 103 LYS cc_start: 0.9171 (ttmm) cc_final: 0.8577 (tptt) REVERT: M 29 PHE cc_start: 0.7747 (t80) cc_final: 0.7271 (t80) REVERT: M 34 MET cc_start: 0.7367 (mmp) cc_final: 0.7159 (mmp) REVERT: M 36 TRP cc_start: 0.7462 (m100) cc_final: 0.7151 (m100) REVERT: W 34 HIS cc_start: 0.6616 (m-70) cc_final: 0.5531 (m-70) REVERT: W 35 TRP cc_start: 0.5952 (m100) cc_final: 0.5664 (m100) REVERT: W 49 TYR cc_start: 0.7692 (p90) cc_final: 0.7291 (p90) REVERT: W 91 TYR cc_start: 0.6114 (t80) cc_final: 0.5877 (t80) outliers start: 67 outliers final: 45 residues processed: 447 average time/residue: 0.1518 time to fit residues: 103.2330 Evaluate side-chains 446 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 395 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 51 ASN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 89 GLN Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 113 optimal weight: 0.0170 chunk 21 optimal weight: 40.0000 chunk 111 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 257 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 overall best weight: 3.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 HIS ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 79 GLN T 51 ASN ** U 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.101139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.062185 restraints weight = 48414.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.064571 restraints weight = 23849.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.066125 restraints weight = 15917.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.067002 restraints weight = 12501.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067625 restraints weight = 10862.944| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20459 Z= 0.201 Angle : 0.636 9.095 27892 Z= 0.333 Chirality : 0.044 0.231 2964 Planarity : 0.004 0.045 3633 Dihedral : 4.794 56.603 2931 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 3.37 % Allowed : 14.77 % Favored : 81.86 % 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: 0.13 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.06 (0.15), residues: 935 loop : -0.51 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 54 TYR 0.026 0.001 TYR W 36 PHE 0.016 0.002 PHE G 67 TRP 0.016 0.001 TRP F 47 HIS 0.003 0.001 HIS W 34 Details of bonding type rmsd covalent geometry : bond 0.00464 (20437) covalent geometry : angle 0.63497 (27848) SS BOND : bond 0.00496 ( 22) SS BOND : angle 1.21494 ( 44) hydrogen bonds : bond 0.03325 ( 768) hydrogen bonds : angle 5.40980 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 403 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7177 (mtp) cc_final: 0.6862 (ppp) REVERT: H 36 TRP cc_start: 0.6820 (m100) cc_final: 0.6209 (m100) REVERT: H 37 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8544 (p) REVERT: H 39 GLN cc_start: 0.5659 (tt0) cc_final: 0.5333 (tt0) REVERT: H 47 TRP cc_start: 0.7554 (t60) cc_final: 0.7347 (t60) REVERT: H 56 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7241 (mmt180) REVERT: H 92 CYS cc_start: 0.7026 (OUTLIER) cc_final: 0.6677 (m) REVERT: H 100 TYR cc_start: 0.8233 (p90) cc_final: 0.7529 (p90) REVERT: L 36 TYR cc_start: 0.7062 (m-80) cc_final: 0.6595 (m-80) REVERT: L 92 ASP cc_start: 0.7962 (t0) cc_final: 0.7421 (t0) REVERT: A 3 GLN cc_start: 0.8175 (tt0) cc_final: 0.7882 (pp30) REVERT: A 32 TYR cc_start: 0.8462 (m-80) cc_final: 0.7680 (m-10) REVERT: A 34 MET cc_start: 0.7652 (mmm) cc_final: 0.7283 (mmm) REVERT: A 46 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 72 ASP cc_start: 0.6779 (t0) cc_final: 0.6474 (t0) REVERT: B 72 ASP cc_start: 0.7915 (t0) cc_final: 0.6924 (t0) REVERT: B 75 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8402 (mmtm) REVERT: B 102 TYR cc_start: 0.8623 (m-80) cc_final: 0.8272 (m-10) REVERT: O 92 ASP cc_start: 0.8921 (t0) cc_final: 0.8708 (t70) REVERT: C 43 LYS cc_start: 0.8890 (mmtm) cc_final: 0.8362 (mmtp) REVERT: Q 79 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: Q 103 LYS cc_start: 0.8073 (tptm) cc_final: 0.7805 (tptt) REVERT: F 43 LYS cc_start: 0.9215 (mmtm) cc_final: 0.9015 (mmtm) REVERT: F 56 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7759 (mtp-110) REVERT: R 5 THR cc_start: 0.9092 (m) cc_final: 0.8866 (p) REVERT: R 79 GLN cc_start: 0.8371 (mp10) cc_final: 0.7581 (mp10) REVERT: G 72 ASP cc_start: 0.7808 (t0) cc_final: 0.7432 (t0) REVERT: G 75 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8770 (mtpp) REVERT: S 83 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7798 (mm-30) REVERT: I 83 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7668 (mtm-85) REVERT: T 5 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9119 (p) REVERT: T 69 THR cc_start: 0.8691 (p) cc_final: 0.8279 (t) REVERT: J 18 LEU cc_start: 0.9029 (tp) cc_final: 0.8689 (mt) REVERT: J 82 MET cc_start: 0.9229 (mtm) cc_final: 0.8470 (mtm) REVERT: U 69 THR cc_start: 0.8858 (p) cc_final: 0.8297 (t) REVERT: U 79 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: K 56 ARG cc_start: 0.8040 (mmt-90) cc_final: 0.7575 (mmm-85) REVERT: K 98 TYR cc_start: 0.8308 (t80) cc_final: 0.8020 (t80) REVERT: V 5 THR cc_start: 0.8351 (m) cc_final: 0.8005 (p) REVERT: V 103 LYS cc_start: 0.9162 (ttmm) cc_final: 0.8574 (tptt) REVERT: V 104 LEU cc_start: 0.9333 (tt) cc_final: 0.9104 (tp) REVERT: M 29 PHE cc_start: 0.7804 (t80) cc_final: 0.7335 (t80) REVERT: M 34 MET cc_start: 0.7318 (mmp) cc_final: 0.7083 (mmp) REVERT: M 36 TRP cc_start: 0.7560 (m100) cc_final: 0.7241 (m100) REVERT: W 34 HIS cc_start: 0.6770 (m-70) cc_final: 0.5434 (m-70) REVERT: W 35 TRP cc_start: 0.6092 (m100) cc_final: 0.5855 (m100) outliers start: 71 outliers final: 53 residues processed: 441 average time/residue: 0.1515 time to fit residues: 101.8342 Evaluate side-chains 440 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 381 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 72 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 51 ASN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 89 GLN Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 158 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 255 optimal weight: 30.0000 chunk 170 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN T 51 ASN U 17 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.101889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.062994 restraints weight = 48517.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.065428 restraints weight = 23776.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.066907 restraints weight = 15783.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.067904 restraints weight = 12419.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.068550 restraints weight = 10705.570| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20459 Z= 0.147 Angle : 0.627 9.780 27892 Z= 0.324 Chirality : 0.043 0.180 2964 Planarity : 0.004 0.044 3633 Dihedral : 4.763 57.022 2931 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.55 % Favored : 94.34 % Rotamer: Outliers : 2.99 % Allowed : 16.19 % Favored : 80.82 % 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: 0.18 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.14 (0.16), residues: 935 loop : -0.50 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG V 93 TYR 0.031 0.001 TYR M 100C PHE 0.011 0.001 PHE G 67 TRP 0.013 0.001 TRP L 35 HIS 0.003 0.001 HIS T 34 Details of bonding type rmsd covalent geometry : bond 0.00341 (20437) covalent geometry : angle 0.62623 (27848) SS BOND : bond 0.00432 ( 22) SS BOND : angle 0.96071 ( 44) hydrogen bonds : bond 0.03179 ( 768) hydrogen bonds : angle 5.33314 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 412 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 34 MET cc_start: 0.7180 (mtp) cc_final: 0.6859 (ppp) REVERT: H 36 TRP cc_start: 0.6823 (m100) cc_final: 0.6216 (m100) REVERT: H 37 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8564 (p) REVERT: H 39 GLN cc_start: 0.5643 (tt0) cc_final: 0.5337 (tt0) REVERT: H 56 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7341 (mmt180) REVERT: H 67 PHE cc_start: 0.8247 (m-10) cc_final: 0.7767 (m-10) REVERT: H 82 MET cc_start: 0.7514 (mtm) cc_final: 0.6934 (mtm) REVERT: H 92 CYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6731 (m) REVERT: H 100 TYR cc_start: 0.8121 (p90) cc_final: 0.7508 (p90) REVERT: L 36 TYR cc_start: 0.7065 (m-80) cc_final: 0.6008 (m-10) REVERT: L 83 GLU cc_start: 0.4475 (tm-30) cc_final: 0.3846 (tp30) REVERT: L 92 ASP cc_start: 0.7748 (t0) cc_final: 0.7474 (t0) REVERT: A 3 GLN cc_start: 0.8298 (tt0) cc_final: 0.8090 (pp30) REVERT: A 32 TYR cc_start: 0.8439 (m-80) cc_final: 0.8182 (m-10) REVERT: A 34 MET cc_start: 0.7608 (mmm) cc_final: 0.7385 (mmt) REVERT: A 46 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 79 TYR cc_start: 0.8055 (m-80) cc_final: 0.7647 (m-80) REVERT: B 72 ASP cc_start: 0.7916 (t0) cc_final: 0.6835 (t0) REVERT: B 75 LYS cc_start: 0.8932 (mmtm) cc_final: 0.8402 (mmtm) REVERT: B 102 TYR cc_start: 0.8625 (m-80) cc_final: 0.8319 (m-80) REVERT: O 92 ASP cc_start: 0.8967 (t0) cc_final: 0.8742 (t70) REVERT: C 43 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8462 (mmtp) REVERT: Q 79 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: Q 103 LYS cc_start: 0.8086 (tptm) cc_final: 0.7835 (tptt) REVERT: F 56 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7754 (mtp-110) REVERT: F 79 TYR cc_start: 0.9003 (m-80) cc_final: 0.8746 (m-10) REVERT: R 5 THR cc_start: 0.9114 (m) cc_final: 0.8900 (p) REVERT: R 69 THR cc_start: 0.9320 (p) cc_final: 0.8881 (t) REVERT: R 78 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8845 (tt) REVERT: R 79 GLN cc_start: 0.8337 (mp10) cc_final: 0.7607 (mp10) REVERT: G 72 ASP cc_start: 0.7830 (t0) cc_final: 0.7471 (t0) REVERT: G 75 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8783 (mtpp) REVERT: I 83 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7720 (mtm-85) REVERT: T 5 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9132 (p) REVERT: T 69 THR cc_start: 0.8670 (p) cc_final: 0.8274 (t) REVERT: J 18 LEU cc_start: 0.9017 (tp) cc_final: 0.8677 (mt) REVERT: J 74 SER cc_start: 0.9275 (m) cc_final: 0.9047 (p) REVERT: J 82 MET cc_start: 0.9206 (mtm) cc_final: 0.8438 (mtm) REVERT: U 69 THR cc_start: 0.8849 (p) cc_final: 0.8333 (t) REVERT: U 78 LEU cc_start: 0.8625 (mt) cc_final: 0.8355 (tp) REVERT: U 79 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: U 81 GLU cc_start: 0.8372 (mp0) cc_final: 0.8005 (pm20) REVERT: K 28 THR cc_start: 0.9330 (m) cc_final: 0.9042 (p) REVERT: K 56 ARG cc_start: 0.8017 (mmt-90) cc_final: 0.7569 (mmm-85) REVERT: K 98 TYR cc_start: 0.8244 (t80) cc_final: 0.7999 (t80) REVERT: V 5 THR cc_start: 0.8440 (m) cc_final: 0.8137 (p) REVERT: V 54 ARG cc_start: 0.8754 (ptt90) cc_final: 0.8390 (ptt180) REVERT: V 79 GLN cc_start: 0.8191 (mm110) cc_final: 0.7833 (mm110) REVERT: V 103 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8687 (tptt) REVERT: M 29 PHE cc_start: 0.7867 (t80) cc_final: 0.7381 (t80) REVERT: M 36 TRP cc_start: 0.7589 (m100) cc_final: 0.7264 (m100) REVERT: W 34 HIS cc_start: 0.6754 (m-70) cc_final: 0.5642 (m-70) outliers start: 63 outliers final: 46 residues processed: 437 average time/residue: 0.1455 time to fit residues: 97.7992 Evaluate side-chains 438 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 385 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 72 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 51 ASN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 89 GLN Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 205 optimal weight: 0.0030 chunk 219 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 overall best weight: 2.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 79 GLN T 51 ASN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.101818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.063068 restraints weight = 48477.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.065489 restraints weight = 23731.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.067019 restraints weight = 15758.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067991 restraints weight = 12324.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.068620 restraints weight = 10640.122| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20459 Z= 0.156 Angle : 0.633 9.348 27892 Z= 0.327 Chirality : 0.043 0.168 2964 Planarity : 0.004 0.060 3633 Dihedral : 4.690 56.508 2931 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.74 % Favored : 94.14 % Rotamer: Outliers : 3.13 % Allowed : 16.43 % Favored : 80.44 % 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: 0.20 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.18 (0.16), residues: 935 loop : -0.50 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 54 TYR 0.048 0.001 TYR V 91 PHE 0.012 0.001 PHE G 67 TRP 0.024 0.001 TRP W 35 HIS 0.003 0.001 HIS T 34 Details of bonding type rmsd covalent geometry : bond 0.00363 (20437) covalent geometry : angle 0.63238 (27848) SS BOND : bond 0.00445 ( 22) SS BOND : angle 1.00358 ( 44) hydrogen bonds : bond 0.03159 ( 768) hydrogen bonds : angle 5.25677 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 399 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8258 (tp) cc_final: 0.7993 (tt) REVERT: H 34 MET cc_start: 0.7159 (mtp) cc_final: 0.6837 (ppp) REVERT: H 36 TRP cc_start: 0.6827 (m100) cc_final: 0.6233 (m100) REVERT: H 37 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8530 (p) REVERT: H 39 GLN cc_start: 0.5647 (tt0) cc_final: 0.5330 (tt0) REVERT: H 67 PHE cc_start: 0.8239 (m-10) cc_final: 0.7860 (m-10) REVERT: H 82 MET cc_start: 0.7364 (mtm) cc_final: 0.6828 (mtm) REVERT: H 92 CYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6646 (m) REVERT: H 100 TYR cc_start: 0.8062 (p90) cc_final: 0.7531 (p90) REVERT: L 36 TYR cc_start: 0.7057 (m-80) cc_final: 0.6028 (m-10) REVERT: L 83 GLU cc_start: 0.4404 (tm-30) cc_final: 0.3768 (tp30) REVERT: L 92 ASP cc_start: 0.7873 (t0) cc_final: 0.7599 (t0) REVERT: A 3 GLN cc_start: 0.8394 (tt0) cc_final: 0.8020 (pp30) REVERT: A 32 TYR cc_start: 0.8456 (m-80) cc_final: 0.7857 (m-10) REVERT: A 46 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 79 TYR cc_start: 0.8133 (m-80) cc_final: 0.7578 (m-80) REVERT: B 72 ASP cc_start: 0.7912 (t0) cc_final: 0.6813 (t0) REVERT: B 75 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8382 (mmtm) REVERT: B 102 TYR cc_start: 0.8533 (m-80) cc_final: 0.8225 (m-80) REVERT: C 43 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8542 (mmtp) REVERT: Q 79 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: F 56 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7771 (mtp-110) REVERT: F 79 TYR cc_start: 0.9000 (m-80) cc_final: 0.8747 (m-10) REVERT: R 5 THR cc_start: 0.9104 (m) cc_final: 0.8895 (p) REVERT: R 69 THR cc_start: 0.9313 (p) cc_final: 0.8874 (t) REVERT: R 78 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8836 (tt) REVERT: R 79 GLN cc_start: 0.8356 (mp10) cc_final: 0.7605 (mp10) REVERT: G 72 ASP cc_start: 0.7874 (t0) cc_final: 0.7460 (t0) REVERT: G 75 LYS cc_start: 0.9139 (mtpp) cc_final: 0.8779 (mtpp) REVERT: T 5 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.9131 (p) REVERT: T 69 THR cc_start: 0.8672 (p) cc_final: 0.8282 (t) REVERT: J 18 LEU cc_start: 0.9015 (tp) cc_final: 0.8696 (mt) REVERT: J 74 SER cc_start: 0.9286 (m) cc_final: 0.9075 (p) REVERT: J 82 MET cc_start: 0.9222 (mtm) cc_final: 0.8425 (mtm) REVERT: U 69 THR cc_start: 0.8834 (p) cc_final: 0.8316 (t) REVERT: U 78 LEU cc_start: 0.8585 (mt) cc_final: 0.8362 (tp) REVERT: K 28 THR cc_start: 0.9337 (m) cc_final: 0.9056 (p) REVERT: K 56 ARG cc_start: 0.8047 (mmt-90) cc_final: 0.7644 (mmm-85) REVERT: K 79 TYR cc_start: 0.8858 (m-80) cc_final: 0.8567 (m-10) REVERT: K 98 TYR cc_start: 0.8196 (t80) cc_final: 0.7994 (t80) REVERT: V 5 THR cc_start: 0.8445 (m) cc_final: 0.8137 (p) REVERT: V 54 ARG cc_start: 0.8772 (ptt90) cc_final: 0.8375 (ptt180) REVERT: V 79 GLN cc_start: 0.8132 (mm110) cc_final: 0.7923 (mm110) REVERT: V 93 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7864 (mtm180) REVERT: V 103 LYS cc_start: 0.9148 (ttmm) cc_final: 0.8583 (tptt) REVERT: M 29 PHE cc_start: 0.7809 (t80) cc_final: 0.7442 (t80) REVERT: M 36 TRP cc_start: 0.7655 (m100) cc_final: 0.7351 (m100) REVERT: W 91 TYR cc_start: 0.6082 (t80) cc_final: 0.5622 (t80) outliers start: 66 outliers final: 50 residues processed: 430 average time/residue: 0.1500 time to fit residues: 98.3356 Evaluate side-chains 441 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 385 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 51 ASN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 48 ILE Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 248 optimal weight: 30.0000 chunk 168 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 11 optimal weight: 30.0000 chunk 89 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 238 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 ASN ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 79 GLN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.063045 restraints weight = 48648.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.065622 restraints weight = 25668.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.065452 restraints weight = 15153.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.065925 restraints weight = 15617.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.066116 restraints weight = 13740.642| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 20459 Z= 0.305 Angle : 0.716 9.725 27892 Z= 0.374 Chirality : 0.046 0.185 2964 Planarity : 0.005 0.047 3633 Dihedral : 5.007 57.997 2931 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.30 % Rotamer: Outliers : 2.80 % Allowed : 17.09 % Favored : 80.10 % 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: -0.09 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.96 (0.15), residues: 1034 loop : -0.80 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 61 TYR 0.031 0.002 TYR M 100C PHE 0.023 0.002 PHE G 67 TRP 0.049 0.002 TRP W 35 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00704 (20437) covalent geometry : angle 0.71352 (27848) SS BOND : bond 0.00634 ( 22) SS BOND : angle 1.57503 ( 44) hydrogen bonds : bond 0.03727 ( 768) hydrogen bonds : angle 5.54934 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 383 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8318 (tp) cc_final: 0.8078 (tt) REVERT: H 34 MET cc_start: 0.7142 (mtp) cc_final: 0.6653 (mmt) REVERT: H 37 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8541 (p) REVERT: H 67 PHE cc_start: 0.8245 (m-10) cc_final: 0.7894 (m-10) REVERT: H 82 MET cc_start: 0.7413 (mtm) cc_final: 0.7098 (mtm) REVERT: H 92 CYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6507 (m) REVERT: H 100 TYR cc_start: 0.8097 (p90) cc_final: 0.7607 (p90) REVERT: L 36 TYR cc_start: 0.7079 (m-80) cc_final: 0.6531 (m-80) REVERT: L 54 ARG cc_start: 0.6663 (ttm-80) cc_final: 0.6168 (ttm-80) REVERT: L 83 GLU cc_start: 0.4385 (tm-30) cc_final: 0.3731 (tp30) REVERT: L 92 ASP cc_start: 0.7833 (t0) cc_final: 0.7512 (t0) REVERT: A 3 GLN cc_start: 0.8522 (tt0) cc_final: 0.8136 (pp30) REVERT: A 32 TYR cc_start: 0.8497 (m-80) cc_final: 0.7868 (m-10) REVERT: A 34 MET cc_start: 0.7679 (mmm) cc_final: 0.7384 (mmm) REVERT: A 46 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7646 (mm-30) REVERT: B 72 ASP cc_start: 0.8014 (t0) cc_final: 0.6890 (t0) REVERT: B 75 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8397 (mmtm) REVERT: B 102 TYR cc_start: 0.8562 (m-80) cc_final: 0.8276 (m-80) REVERT: O 27 ASN cc_start: 0.9053 (p0) cc_final: 0.8576 (p0) REVERT: O 79 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7434 (mp-120) REVERT: Q 79 GLN cc_start: 0.7992 (mp10) cc_final: 0.7658 (mp10) REVERT: F 56 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7757 (mtp-110) REVERT: R 78 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9104 (tt) REVERT: G 72 ASP cc_start: 0.7956 (t0) cc_final: 0.7605 (t0) REVERT: G 75 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8912 (mtpp) REVERT: I 83 ARG cc_start: 0.8293 (mtm110) cc_final: 0.7343 (mtm-85) REVERT: T 5 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9107 (p) REVERT: T 69 THR cc_start: 0.8813 (p) cc_final: 0.8371 (t) REVERT: J 18 LEU cc_start: 0.9024 (tp) cc_final: 0.8774 (mt) REVERT: J 72 ASP cc_start: 0.7136 (t0) cc_final: 0.6903 (t0) REVERT: J 74 SER cc_start: 0.9302 (m) cc_final: 0.9053 (p) REVERT: J 75 LYS cc_start: 0.9371 (mtpp) cc_final: 0.9164 (mtpp) REVERT: U 69 THR cc_start: 0.8872 (p) cc_final: 0.8328 (t) REVERT: U 78 LEU cc_start: 0.8620 (mt) cc_final: 0.8416 (tp) REVERT: K 56 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7712 (mmm-85) REVERT: K 98 TYR cc_start: 0.8345 (t80) cc_final: 0.8090 (t80) REVERT: V 5 THR cc_start: 0.8373 (m) cc_final: 0.8032 (p) REVERT: V 54 ARG cc_start: 0.8900 (ptt90) cc_final: 0.8567 (ptt180) REVERT: V 91 TYR cc_start: 0.8356 (t80) cc_final: 0.7902 (t80) REVERT: V 92 ASP cc_start: 0.8496 (t70) cc_final: 0.8192 (m-30) REVERT: V 93 ARG cc_start: 0.8297 (mtm110) cc_final: 0.7766 (mtm180) REVERT: V 103 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8662 (tptt) REVERT: V 104 LEU cc_start: 0.9449 (tt) cc_final: 0.9136 (tp) REVERT: M 29 PHE cc_start: 0.7891 (t80) cc_final: 0.7476 (t80) REVERT: M 36 TRP cc_start: 0.7772 (m100) cc_final: 0.7462 (m100) REVERT: W 91 TYR cc_start: 0.6346 (t80) cc_final: 0.5998 (t80) outliers start: 59 outliers final: 48 residues processed: 413 average time/residue: 0.1543 time to fit residues: 96.6441 Evaluate side-chains 424 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 371 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 72 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 51 ASN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 252 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 41 optimal weight: 30.0000 chunk 12 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 249 optimal weight: 30.0000 chunk 188 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN P 79 GLN U 79 GLN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.099292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.061109 restraints weight = 48927.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.063530 restraints weight = 23479.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.065003 restraints weight = 15462.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.066008 restraints weight = 12105.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.066643 restraints weight = 10402.696| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20459 Z= 0.315 Angle : 0.728 9.279 27892 Z= 0.380 Chirality : 0.046 0.176 2964 Planarity : 0.005 0.046 3633 Dihedral : 5.161 59.824 2931 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.30 % Rotamer: Outliers : 2.75 % Allowed : 17.43 % Favored : 79.82 % 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 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 0.89 (0.15), residues: 968 loop : -1.02 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 66 TYR 0.029 0.002 TYR M 100C PHE 0.022 0.002 PHE G 67 TRP 0.039 0.002 TRP W 35 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00727 (20437) covalent geometry : angle 0.72585 (27848) SS BOND : bond 0.00622 ( 22) SS BOND : angle 1.45327 ( 44) hydrogen bonds : bond 0.03785 ( 768) hydrogen bonds : angle 5.74194 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 376 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8588 (p) REVERT: H 39 GLN cc_start: 0.6013 (tt0) cc_final: 0.5811 (tt0) REVERT: H 67 PHE cc_start: 0.8287 (m-10) cc_final: 0.7937 (m-10) REVERT: H 82 MET cc_start: 0.7444 (mtm) cc_final: 0.7089 (mtm) REVERT: H 100 TYR cc_start: 0.8095 (p90) cc_final: 0.7621 (p90) REVERT: L 36 TYR cc_start: 0.7036 (m-80) cc_final: 0.6464 (m-80) REVERT: L 54 ARG cc_start: 0.6897 (ttm-80) cc_final: 0.6453 (ttm-80) REVERT: L 83 GLU cc_start: 0.4461 (tm-30) cc_final: 0.3787 (tp30) REVERT: L 92 ASP cc_start: 0.7775 (t0) cc_final: 0.7449 (t0) REVERT: A 3 GLN cc_start: 0.8601 (tt0) cc_final: 0.8222 (pp30) REVERT: A 32 TYR cc_start: 0.8485 (m-80) cc_final: 0.7921 (m-10) REVERT: A 46 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 79 TYR cc_start: 0.8225 (m-80) cc_final: 0.7680 (m-80) REVERT: B 72 ASP cc_start: 0.8017 (t0) cc_final: 0.6938 (t0) REVERT: B 75 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8398 (mmtm) REVERT: B 102 TYR cc_start: 0.8561 (m-80) cc_final: 0.8228 (m-80) REVERT: O 27 ASN cc_start: 0.9042 (p0) cc_final: 0.8549 (p0) REVERT: O 79 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7678 (mp-120) REVERT: C 43 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8357 (mmtp) REVERT: Q 79 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: F 56 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7802 (mtp-110) REVERT: G 72 ASP cc_start: 0.7956 (t0) cc_final: 0.7586 (t0) REVERT: G 75 LYS cc_start: 0.9132 (mtpp) cc_final: 0.8895 (mtpp) REVERT: I 83 ARG cc_start: 0.8403 (mtm110) cc_final: 0.7478 (mtm-85) REVERT: T 5 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.9142 (p) REVERT: T 69 THR cc_start: 0.8815 (p) cc_final: 0.8467 (t) REVERT: J 18 LEU cc_start: 0.9034 (tp) cc_final: 0.8801 (mt) REVERT: U 69 THR cc_start: 0.8862 (p) cc_final: 0.8341 (t) REVERT: K 56 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.7739 (mmm-85) REVERT: K 98 TYR cc_start: 0.8439 (t80) cc_final: 0.8177 (t80) REVERT: V 5 THR cc_start: 0.8244 (m) cc_final: 0.7851 (p) REVERT: V 54 ARG cc_start: 0.8920 (ptt90) cc_final: 0.8619 (ptt180) REVERT: V 91 TYR cc_start: 0.8500 (t80) cc_final: 0.8267 (t80) REVERT: V 93 ARG cc_start: 0.8401 (mtm110) cc_final: 0.7909 (mtm180) REVERT: V 103 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8684 (tptt) REVERT: M 29 PHE cc_start: 0.7930 (t80) cc_final: 0.7551 (t80) REVERT: M 36 TRP cc_start: 0.7636 (m100) cc_final: 0.7377 (m100) REVERT: W 91 TYR cc_start: 0.6249 (t80) cc_final: 0.5896 (t80) outliers start: 58 outliers final: 48 residues processed: 408 average time/residue: 0.1554 time to fit residues: 95.1345 Evaluate side-chains 416 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 364 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 72 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 56 ARG Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain S residue 51 ASN Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 18 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 106 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain V residue 33 VAL Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 82 MET Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 182 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 ASN ** O 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 GLN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.062042 restraints weight = 49301.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.064364 restraints weight = 24403.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.065876 restraints weight = 16296.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.066751 restraints weight = 12820.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.067218 restraints weight = 11115.602| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20459 Z= 0.162 Angle : 0.674 9.579 27892 Z= 0.345 Chirality : 0.044 0.199 2964 Planarity : 0.004 0.043 3633 Dihedral : 4.924 59.507 2931 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 2.56 % Allowed : 18.38 % Favored : 79.06 % 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: -0.19 (0.16), residues: 2596 helix: None (None), residues: 0 sheet: 1.08 (0.16), residues: 869 loop : -0.82 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 61 TYR 0.030 0.001 TYR M 100C PHE 0.024 0.002 PHE H 29 TRP 0.038 0.002 TRP W 35 HIS 0.004 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00376 (20437) covalent geometry : angle 0.67315 (27848) SS BOND : bond 0.00498 ( 22) SS BOND : angle 0.98240 ( 44) hydrogen bonds : bond 0.03321 ( 768) hydrogen bonds : angle 5.49616 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4196.81 seconds wall clock time: 72 minutes 55.44 seconds (4375.44 seconds total)