Starting phenix.real_space_refine on Thu Feb 5 21:57:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uo6_64375/02_2026/9uo6_64375.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uo6_64375/02_2026/9uo6_64375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uo6_64375/02_2026/9uo6_64375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uo6_64375/02_2026/9uo6_64375.map" model { file = "/net/cci-nas-00/data/ceres_data/9uo6_64375/02_2026/9uo6_64375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uo6_64375/02_2026/9uo6_64375.cif" } resolution = 3.29 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= 0.001 sd= 0.034 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 108 5.16 5 C 12888 2.51 5 N 3186 2.21 5 O 3894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20076 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1681 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "B" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1665 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "A" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1681 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "D" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1665 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "E" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1681 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "F" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1665 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "G" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1681 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "H" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1665 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "I" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1681 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "J" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1665 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "K" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1681 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 13, 'TRANS': 199} Chain: "L" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1665 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 20076 At special positions: 0 Unit cell: (57.78, 190.46, 196.88, 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 108 16.00 O 3894 8.00 N 3186 7.00 C 12888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 83 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS B 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 83 " distance=2.03 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS D 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 192 " distance=2.02 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 83 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS F 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 83 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 83 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS H 71 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 83 " distance=2.03 Simple disulfide: pdb=" SG CYS H 131 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 83 " distance=2.03 Simple disulfide: pdb=" SG CYS I 71 " - pdb=" SG CYS J 71 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 192 " distance=2.02 Simple disulfide: pdb=" SG CYS J 24 " - pdb=" SG CYS J 83 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 83 " distance=2.03 Simple disulfide: pdb=" SG CYS K 71 " - pdb=" SG CYS L 71 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 83 " distance=2.03 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 192 " distance=2.02 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: 1.63 Conformation dependent library (CDL) restraints added in 666.2 milliseconds 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4824 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 72 sheets defined 10.5% alpha, 42.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 180 through 186 removed outlier: 3.515A pdb=" N TRP C 184 " --> pdb=" O PRO C 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.507A pdb=" N GLU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'D' and resid 10 through 16 Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 180 through 187 removed outlier: 3.572A pdb=" N TRP D 184 " --> pdb=" O PRO D 180 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 16 Processing helix chain 'E' and resid 71 through 77 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'F' and resid 10 through 15 Processing helix chain 'F' and resid 72 through 77 removed outlier: 3.688A pdb=" N SER F 77 " --> pdb=" O GLU F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 185 removed outlier: 3.611A pdb=" N ASN F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 16 removed outlier: 3.531A pdb=" N TYR G 15 " --> pdb=" O PHE G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 77 Processing helix chain 'G' and resid 180 through 186 removed outlier: 3.757A pdb=" N TRP G 184 " --> pdb=" O PRO G 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 180 through 186 removed outlier: 3.520A pdb=" N TRP H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 16 Processing helix chain 'I' and resid 71 through 76 removed outlier: 3.568A pdb=" N GLU I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 180 through 187 removed outlier: 3.902A pdb=" N GLY I 187 " --> pdb=" O LYS I 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 16 Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 117 through 126 removed outlier: 3.592A pdb=" N GLU J 120 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU J 121 " --> pdb=" O ALA J 118 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE J 122 " --> pdb=" O GLN J 119 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN J 124 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 180 through 187 removed outlier: 3.555A pdb=" N TRP J 184 " --> pdb=" O PRO J 180 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 16 Processing helix chain 'K' and resid 71 through 77 removed outlier: 3.750A pdb=" N TRP K 75 " --> pdb=" O CYS K 71 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 71 through 77' Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'L' and resid 11 through 16 Processing helix chain 'L' and resid 71 through 76 Processing helix chain 'L' and resid 153 through 155 No H-bonds generated for 'chain 'L' and resid 153 through 155' Processing helix chain 'L' and resid 180 through 186 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.741A pdb=" N LEU C 25 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 23 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 69 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU C 48 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.741A pdb=" N LEU C 25 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 23 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 36 through 41 removed outlier: 3.520A pdb=" N ARG C 86 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 84 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 40 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 85 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.520A pdb=" N SER C 175 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AA6, first strand: chain 'C' and resid 142 through 146 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.978A pdb=" N SER B 66 " --> pdb=" O CYS B 24 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 69 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU B 48 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 41 removed outlier: 3.549A pdb=" N CYS B 83 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 85 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 94 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AB1, first strand: chain 'B' and resid 110 through 114 removed outlier: 3.674A pdb=" N SER B 175 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AB3, first strand: chain 'B' and resid 142 through 146 removed outlier: 3.554A pdb=" N GLN B 206 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.534A pdb=" N CYS A 24 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 66 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 69 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 48 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.534A pdb=" N CYS A 24 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 66 " --> pdb=" O CYS A 24 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 40 through 41 Processing sheet with id=AB7, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.769A pdb=" N ILE A 130 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.769A pdb=" N ILE A 130 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 150 through 151 removed outlier: 4.236A pdb=" N VAL A 150 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.558A pdb=" N SER D 69 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU D 48 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 36 through 41 removed outlier: 3.514A pdb=" N GLU D 40 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 82 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS D 96 " --> pdb=" O CYS D 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D 85 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 94 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'D' and resid 110 through 114 removed outlier: 5.096A pdb=" N TYR D 171 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 151 through 152 removed outlier: 4.765A pdb=" N TRP D 145 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.526A pdb=" N SER E 66 " --> pdb=" O CYS E 24 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER E 69 " --> pdb=" O GLU E 48 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU E 48 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 36 through 41 removed outlier: 3.665A pdb=" N GLU E 40 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER E 82 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS E 83 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS E 96 " --> pdb=" O CYS E 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 85 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 94 " --> pdb=" O VAL E 85 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AD1, first strand: chain 'E' and resid 110 through 114 removed outlier: 3.592A pdb=" N LEU E 129 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER E 175 " --> pdb=" O CYS E 131 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 176 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 110 through 114 removed outlier: 5.149A pdb=" N TYR E 171 " --> pdb=" O GLY E 135 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 142 through 146 Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.682A pdb=" N THR F 23 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER F 66 " --> pdb=" O CYS F 24 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER F 69 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU F 48 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.682A pdb=" N THR F 23 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER F 66 " --> pdb=" O CYS F 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 36 through 41 removed outlier: 3.507A pdb=" N VAL F 94 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 110 through 114 removed outlier: 3.581A pdb=" N SER F 175 " --> pdb=" O CYS F 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS F 176 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE F 158 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AD9, first strand: chain 'F' and resid 150 through 152 removed outlier: 4.740A pdb=" N TRP F 145 " --> pdb=" O ILE F 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.560A pdb=" N THR G 23 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER G 66 " --> pdb=" O CYS G 24 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL G 50 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER G 69 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU G 48 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 36 through 41 removed outlier: 3.574A pdb=" N CYS G 83 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL G 85 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL G 94 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 55 through 57 Processing sheet with id=AE4, first strand: chain 'G' and resid 110 through 114 removed outlier: 3.533A pdb=" N LEU G 129 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER G 175 " --> pdb=" O CYS G 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 110 through 114 removed outlier: 5.413A pdb=" N TYR G 171 " --> pdb=" O GLY G 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.612A pdb=" N THR H 23 " --> pdb=" O LEU H 7 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA H 20 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER H 28 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR H 62 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 69 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU H 48 " --> pdb=" O SER H 69 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.612A pdb=" N THR H 23 " --> pdb=" O LEU H 7 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA H 20 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER H 28 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N TYR H 62 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 36 through 41 removed outlier: 4.001A pdb=" N VAL H 85 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL H 94 " --> pdb=" O VAL H 85 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 110 through 114 removed outlier: 3.700A pdb=" N ILE H 130 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 110 through 114 removed outlier: 3.700A pdb=" N ILE H 130 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 151 through 152 removed outlier: 4.752A pdb=" N TRP H 145 " --> pdb=" O ILE H 152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.905A pdb=" N SER I 66 " --> pdb=" O CYS I 24 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER I 69 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU I 48 " --> pdb=" O SER I 69 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 4 through 7 removed outlier: 4.263A pdb=" N SER I 28 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR I 62 " --> pdb=" O SER I 28 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 36 through 41 removed outlier: 3.526A pdb=" N ARG I 86 " --> pdb=" O ASP I 36 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS I 96 " --> pdb=" O CYS I 83 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL I 85 " --> pdb=" O VAL I 94 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL I 94 " --> pdb=" O VAL I 85 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 110 through 114 removed outlier: 3.661A pdb=" N SER I 175 " --> pdb=" O CYS I 131 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 110 through 114 removed outlier: 5.624A pdb=" N TYR I 171 " --> pdb=" O GLY I 135 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 151 through 152 removed outlier: 4.808A pdb=" N TRP I 145 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE I 208 " --> pdb=" O PHE I 190 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.559A pdb=" N LEU J 25 " --> pdb=" O TYR J 5 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 36 through 41 removed outlier: 3.539A pdb=" N THR J 84 " --> pdb=" O SER J 38 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER J 82 " --> pdb=" O GLU J 40 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS J 83 " --> pdb=" O LYS J 96 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS J 96 " --> pdb=" O CYS J 83 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL J 85 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL J 94 " --> pdb=" O VAL J 85 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 55 through 57 Processing sheet with id=AG4, first strand: chain 'J' and resid 110 through 114 Processing sheet with id=AG5, first strand: chain 'J' and resid 110 through 114 Processing sheet with id=AG6, first strand: chain 'J' and resid 150 through 151 removed outlier: 3.726A pdb=" N VAL J 150 " --> pdb=" O GLN J 147 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.659A pdb=" N SER K 66 " --> pdb=" O CYS K 24 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 36 through 41 removed outlier: 3.506A pdb=" N CYS K 83 " --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 55 through 57 Processing sheet with id=AH1, first strand: chain 'K' and resid 110 through 114 removed outlier: 3.629A pdb=" N ILE K 130 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER K 175 " --> pdb=" O CYS K 131 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 110 through 114 removed outlier: 3.629A pdb=" N ILE K 130 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR K 171 " --> pdb=" O GLY K 135 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 150 through 152 removed outlier: 3.686A pdb=" N VAL K 150 " --> pdb=" O GLN K 147 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TRP K 145 " --> pdb=" O ILE K 152 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.768A pdb=" N THR L 23 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA L 20 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU L 48 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.768A pdb=" N THR L 23 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA L 20 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 36 through 41 removed outlier: 3.608A pdb=" N SER L 38 " --> pdb=" O THR L 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS L 83 " --> pdb=" O LYS L 96 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS L 96 " --> pdb=" O CYS L 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL L 85 " --> pdb=" O VAL L 94 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 110 through 114 removed outlier: 3.876A pdb=" N VAL L 127 " --> pdb=" O ILE L 179 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE L 179 " --> pdb=" O VAL L 127 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 110 through 114 removed outlier: 5.554A pdb=" N TYR L 171 " --> pdb=" O GLY L 135 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 150 through 151 removed outlier: 4.189A pdb=" N VAL L 150 " --> pdb=" O GLN L 147 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2109 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: 3.04 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6354 1.34 - 1.46: 4404 1.46 - 1.58: 9666 1.58 - 1.70: 0 1.70 - 1.81: 156 Bond restraints: 20580 Sorted by residual: bond pdb=" N GLU G 125 " pdb=" CA GLU G 125 " ideal model delta sigma weight residual 1.454 1.503 -0.050 1.34e-02 5.57e+03 1.38e+01 bond pdb=" N PHE H 16 " pdb=" CA PHE H 16 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.32e-02 5.74e+03 1.29e+01 bond pdb=" N ASN H 19 " pdb=" CA ASN H 19 " ideal model delta sigma weight residual 1.461 1.503 -0.042 1.19e-02 7.06e+03 1.25e+01 bond pdb=" N ILE L 122 " pdb=" CA ILE L 122 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" CA SER H 17 " pdb=" CB SER H 17 " ideal model delta sigma weight residual 1.536 1.495 0.042 1.46e-02 4.69e+03 8.23e+00 ... (remaining 20575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 27047 1.64 - 3.28: 766 3.28 - 4.92: 140 4.92 - 6.56: 40 6.56 - 8.20: 9 Bond angle restraints: 28002 Sorted by residual: angle pdb=" CA PHE H 16 " pdb=" CB PHE H 16 " pdb=" CG PHE H 16 " ideal model delta sigma weight residual 113.80 105.60 8.20 1.00e+00 1.00e+00 6.72e+01 angle pdb=" N GLU F 120 " pdb=" CA GLU F 120 " pdb=" C GLU F 120 " ideal model delta sigma weight residual 112.93 106.56 6.37 1.12e+00 7.97e-01 3.23e+01 angle pdb=" N SER H 17 " pdb=" CA SER H 17 " pdb=" C SER H 17 " ideal model delta sigma weight residual 114.39 106.94 7.45 1.45e+00 4.76e-01 2.64e+01 angle pdb=" C LEU F 129 " pdb=" N ILE F 130 " pdb=" CA ILE F 130 " ideal model delta sigma weight residual 122.93 117.79 5.14 1.26e+00 6.30e-01 1.67e+01 angle pdb=" CA ARG H 18 " pdb=" C ARG H 18 " pdb=" O ARG H 18 " ideal model delta sigma weight residual 121.65 116.94 4.71 1.17e+00 7.31e-01 1.62e+01 ... (remaining 27997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11156 17.95 - 35.90: 1060 35.90 - 53.85: 153 53.85 - 71.80: 25 71.80 - 89.74: 26 Dihedral angle restraints: 12420 sinusoidal: 4986 harmonic: 7434 Sorted by residual: dihedral pdb=" CD ARG H 18 " pdb=" NE ARG H 18 " pdb=" CZ ARG H 18 " pdb=" NH1 ARG H 18 " ideal model delta sinusoidal sigma weight residual 0.00 -78.31 78.31 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS I 24 " pdb=" SG CYS I 24 " pdb=" SG CYS I 83 " pdb=" CB CYS I 83 " ideal model delta sinusoidal sigma weight residual 93.00 153.41 -60.41 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CA LEU C 201 " pdb=" C LEU C 201 " pdb=" N TYR C 202 " pdb=" CA TYR C 202 " ideal model delta harmonic sigma weight residual -180.00 -155.29 -24.71 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 12417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2577 0.061 - 0.123: 498 0.123 - 0.184: 53 0.184 - 0.246: 10 0.246 - 0.307: 6 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CA ILE J 122 " pdb=" N ILE J 122 " pdb=" C ILE J 122 " pdb=" CB ILE J 122 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA VAL F 127 " pdb=" N VAL F 127 " pdb=" C VAL F 127 " pdb=" CB VAL F 127 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA PHE H 16 " pdb=" N PHE H 16 " pdb=" C PHE H 16 " pdb=" CB PHE H 16 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3141 not shown) Planarity restraints: 3594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 18 " 1.118 9.50e-02 1.11e+02 5.01e-01 1.51e+02 pdb=" NE ARG H 18 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG H 18 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG H 18 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG H 18 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 15 " 0.024 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C TYR H 15 " -0.081 2.00e-02 2.50e+03 pdb=" O TYR H 15 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE H 16 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 124 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C GLN G 124 " 0.059 2.00e-02 2.50e+03 pdb=" O GLN G 124 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU G 125 " -0.020 2.00e-02 2.50e+03 ... (remaining 3591 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 49 2.45 - 3.06: 11932 3.06 - 3.68: 29368 3.68 - 4.29: 43575 4.29 - 4.90: 73178 Nonbonded interactions: 158102 Sorted by model distance: nonbonded pdb=" O GLN G 119 " pdb=" SD MET G 126 " model vdw 1.840 3.400 nonbonded pdb=" OH TYR A 15 " pdb=" OE1 GLU A 76 " model vdw 2.277 3.040 nonbonded pdb=" O SER F 38 " pdb=" OG1 THR F 84 " model vdw 2.282 3.040 nonbonded pdb=" OG SER E 153 " pdb=" OD1 ASP E 155 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR A 10 " pdb=" OE2 GLU A 140 " model vdw 2.294 3.040 ... (remaining 158097 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 210) selection = chain 'B' selection = (chain 'C' and resid 1 through 210) selection = chain 'D' selection = (chain 'E' and resid 1 through 210) selection = chain 'F' selection = (chain 'G' and resid 1 through 210) selection = chain 'H' selection = (chain 'I' and resid 1 through 210) selection = chain 'J' selection = (chain 'K' and resid 1 through 210) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 : 0.004 0.050 20610 Z= 0.175 Angle : 0.675 8.197 28062 Z= 0.369 Chirality : 0.051 0.307 3144 Planarity : 0.010 0.501 3594 Dihedral : 14.140 89.744 7506 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 2514 helix: -3.21 (0.21), residues: 240 sheet: -0.69 (0.17), residues: 988 loop : -0.62 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 18 TYR 0.026 0.001 TYR K 174 PHE 0.029 0.002 PHE H 16 TRP 0.011 0.001 TRP H 75 HIS 0.003 0.001 HIS J 196 Details of bonding type rmsd covalent geometry : bond 0.00354 (20580) covalent geometry : angle 0.67503 (28002) SS BOND : bond 0.00363 ( 30) SS BOND : angle 0.78677 ( 60) hydrogen bonds : bond 0.28253 ( 694) hydrogen bonds : angle 11.78838 ( 2109) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 ASP cc_start: 0.8012 (m-30) cc_final: 0.7801 (m-30) REVERT: A 29 MET cc_start: 0.6007 (mtp) cc_final: 0.5756 (mtp) REVERT: A 74 ASP cc_start: 0.7987 (m-30) cc_final: 0.7709 (m-30) REVERT: A 110 ASP cc_start: 0.8452 (m-30) cc_final: 0.8189 (m-30) REVERT: D 36 ASP cc_start: 0.7693 (p0) cc_final: 0.7405 (p0) REVERT: E 110 ASP cc_start: 0.7760 (m-30) cc_final: 0.7457 (m-30) REVERT: E 112 TYR cc_start: 0.7932 (m-80) cc_final: 0.7356 (m-80) REVERT: E 171 TYR cc_start: 0.8161 (m-80) cc_final: 0.7684 (m-80) REVERT: F 102 ASN cc_start: 0.7298 (t0) cc_final: 0.6884 (t0) REVERT: F 154 GLU cc_start: 0.7744 (mp0) cc_final: 0.7469 (mm-30) REVERT: G 120 GLU cc_start: 0.7328 (pm20) cc_final: 0.7076 (pm20) REVERT: G 126 MET cc_start: 0.4265 (ttm) cc_final: 0.3204 (tpp) REVERT: G 147 GLN cc_start: 0.6975 (tp-100) cc_final: 0.6737 (tp40) REVERT: G 188 ASP cc_start: 0.7089 (p0) cc_final: 0.6291 (p0) REVERT: H 43 LYS cc_start: 0.7462 (ttmm) cc_final: 0.6890 (tppt) REVERT: H 68 LEU cc_start: 0.6597 (tp) cc_final: 0.6194 (tp) REVERT: H 99 PHE cc_start: 0.7188 (p90) cc_final: 0.6863 (p90) REVERT: H 112 TYR cc_start: 0.7959 (m-80) cc_final: 0.7755 (m-80) REVERT: H 137 ASN cc_start: 0.7988 (t0) cc_final: 0.7707 (t0) REVERT: J 47 LEU cc_start: 0.7621 (tp) cc_final: 0.7257 (mm) REVERT: L 29 MET cc_start: 0.6492 (mtm) cc_final: 0.6009 (mtp) REVERT: L 43 LYS cc_start: 0.8141 (ptmm) cc_final: 0.7811 (ptmm) REVERT: L 57 HIS cc_start: 0.7401 (m170) cc_final: 0.7169 (m90) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.1201 time to fit residues: 79.4937 Evaluate side-chains 246 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS H 123 GLN J 119 GLN J 147 GLN J 206 GLN K 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.212599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.156714 restraints weight = 26648.559| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.03 r_work: 0.3698 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20610 Z= 0.222 Angle : 0.667 10.295 28062 Z= 0.353 Chirality : 0.049 0.259 3144 Planarity : 0.005 0.099 3594 Dihedral : 5.150 26.804 2646 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.61 % Allowed : 9.25 % Favored : 89.14 % 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: -1.27 (0.17), residues: 2514 helix: -2.39 (0.26), residues: 246 sheet: -0.66 (0.16), residues: 1070 loop : -0.49 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 18 TYR 0.027 0.002 TYR K 174 PHE 0.031 0.002 PHE G 157 TRP 0.010 0.001 TRP H 75 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00528 (20580) covalent geometry : angle 0.66586 (28002) SS BOND : bond 0.00634 ( 30) SS BOND : angle 0.95836 ( 60) hydrogen bonds : bond 0.05224 ( 694) hydrogen bonds : angle 7.47154 ( 2109) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 5 TYR cc_start: 0.6341 (m-80) cc_final: 0.5825 (t80) REVERT: B 13 ASP cc_start: 0.8281 (m-30) cc_final: 0.8031 (m-30) REVERT: B 73 GLU cc_start: 0.7199 (mp0) cc_final: 0.6803 (mp0) REVERT: A 71 CYS cc_start: 0.6207 (m) cc_final: 0.5658 (m) REVERT: A 74 ASP cc_start: 0.8232 (m-30) cc_final: 0.7988 (m-30) REVERT: A 209 ASP cc_start: 0.8214 (p0) cc_final: 0.7894 (p0) REVERT: E 5 TYR cc_start: 0.3045 (t80) cc_final: 0.2776 (m-80) REVERT: E 74 ASP cc_start: 0.7392 (m-30) cc_final: 0.7190 (m-30) REVERT: F 102 ASN cc_start: 0.7177 (t0) cc_final: 0.6874 (t0) REVERT: F 123 GLN cc_start: 0.7058 (tp40) cc_final: 0.6835 (pm20) REVERT: F 154 GLU cc_start: 0.7873 (mp0) cc_final: 0.7602 (mm-30) REVERT: H 17 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.7208 (p) REVERT: H 43 LYS cc_start: 0.7650 (ttmm) cc_final: 0.7424 (ttpt) REVERT: H 68 LEU cc_start: 0.6558 (tp) cc_final: 0.6104 (tp) REVERT: I 40 GLU cc_start: 0.7434 (tp30) cc_final: 0.7219 (tp30) REVERT: I 205 GLN cc_start: 0.8858 (pm20) cc_final: 0.8605 (pt0) REVERT: J 47 LEU cc_start: 0.7599 (tp) cc_final: 0.7250 (mm) REVERT: L 43 LYS cc_start: 0.8275 (ptmm) cc_final: 0.7948 (ptmm) REVERT: L 99 PHE cc_start: 0.8112 (p90) cc_final: 0.7752 (p90) REVERT: L 169 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8195 (tp-100) outliers start: 37 outliers final: 27 residues processed: 301 average time/residue: 0.1268 time to fit residues: 61.4395 Evaluate side-chains 265 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 28 optimal weight: 0.7980 chunk 182 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 188 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS E 205 GLN K 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.214070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.157761 restraints weight = 26573.553| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.00 r_work: 0.3744 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20610 Z= 0.151 Angle : 0.596 9.539 28062 Z= 0.314 Chirality : 0.047 0.204 3144 Planarity : 0.005 0.068 3594 Dihedral : 4.979 25.158 2646 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.27 % Allowed : 11.78 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2514 helix: -2.00 (0.28), residues: 246 sheet: -0.59 (0.16), residues: 1070 loop : -0.42 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 18 TYR 0.020 0.001 TYR K 174 PHE 0.023 0.002 PHE G 157 TRP 0.012 0.001 TRP F 75 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00356 (20580) covalent geometry : angle 0.59482 (28002) SS BOND : bond 0.00493 ( 30) SS BOND : angle 0.95187 ( 60) hydrogen bonds : bond 0.04165 ( 694) hydrogen bonds : angle 6.58522 ( 2109) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ARG cc_start: 0.8123 (ttp-170) cc_final: 0.7864 (ttp-170) REVERT: C 49 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: B 5 TYR cc_start: 0.6405 (m-80) cc_final: 0.5753 (t80) REVERT: B 13 ASP cc_start: 0.8220 (m-30) cc_final: 0.7993 (m-30) REVERT: B 73 GLU cc_start: 0.7338 (mp0) cc_final: 0.6938 (mp0) REVERT: B 121 LEU cc_start: 0.6602 (mt) cc_final: 0.6304 (pt) REVERT: A 71 CYS cc_start: 0.5906 (m) cc_final: 0.5359 (m) REVERT: A 209 ASP cc_start: 0.8162 (p0) cc_final: 0.7882 (p0) REVERT: F 126 MET cc_start: 0.7199 (mpp) cc_final: 0.6563 (tmm) REVERT: F 154 GLU cc_start: 0.7807 (mp0) cc_final: 0.7535 (mm-30) REVERT: G 123 GLN cc_start: 0.8046 (pm20) cc_final: 0.7615 (mm-40) REVERT: H 17 SER cc_start: 0.7243 (OUTLIER) cc_final: 0.6849 (p) REVERT: H 68 LEU cc_start: 0.6554 (tp) cc_final: 0.6094 (tp) REVERT: J 29 MET cc_start: 0.6102 (ttm) cc_final: 0.5742 (tpp) REVERT: J 47 LEU cc_start: 0.7629 (tp) cc_final: 0.7256 (mm) REVERT: K 103 GLU cc_start: 0.6645 (tt0) cc_final: 0.6406 (tt0) REVERT: L 57 HIS cc_start: 0.7562 (m90) cc_final: 0.7347 (m90) REVERT: L 169 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8114 (tp-100) outliers start: 52 outliers final: 41 residues processed: 303 average time/residue: 0.1245 time to fit residues: 60.7998 Evaluate side-chains 264 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 207 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 136 optimal weight: 0.1980 chunk 242 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN E 205 GLN F 101 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN H 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.213261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157824 restraints weight = 26533.884| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.76 r_work: 0.3763 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20610 Z= 0.167 Angle : 0.597 12.141 28062 Z= 0.310 Chirality : 0.047 0.265 3144 Planarity : 0.005 0.073 3594 Dihedral : 4.907 25.298 2646 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.66 % Allowed : 14.01 % Favored : 83.33 % 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: -0.99 (0.17), residues: 2514 helix: -1.79 (0.29), residues: 242 sheet: -0.55 (0.15), residues: 1082 loop : -0.30 (0.19), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 18 TYR 0.021 0.001 TYR K 174 PHE 0.024 0.002 PHE H 16 TRP 0.013 0.001 TRP F 39 HIS 0.003 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00401 (20580) covalent geometry : angle 0.59579 (28002) SS BOND : bond 0.00478 ( 30) SS BOND : angle 0.95016 ( 60) hydrogen bonds : bond 0.03756 ( 694) hydrogen bonds : angle 6.19241 ( 2109) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 247 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7858 (ttp-170) REVERT: C 49 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6241 (m-80) REVERT: B 73 GLU cc_start: 0.7298 (mp0) cc_final: 0.7023 (mp0) REVERT: A 71 CYS cc_start: 0.5959 (m) cc_final: 0.5627 (m) REVERT: A 209 ASP cc_start: 0.8022 (p0) cc_final: 0.7759 (p0) REVERT: E 5 TYR cc_start: 0.4534 (OUTLIER) cc_final: 0.3938 (m-80) REVERT: E 74 ASP cc_start: 0.7202 (m-30) cc_final: 0.7002 (m-30) REVERT: F 126 MET cc_start: 0.7060 (mpp) cc_final: 0.6544 (tmm) REVERT: H 68 LEU cc_start: 0.6644 (tp) cc_final: 0.6188 (tp) REVERT: I 171 TYR cc_start: 0.8605 (m-80) cc_final: 0.7489 (m-80) REVERT: J 29 MET cc_start: 0.5932 (ttm) cc_final: 0.5661 (tpp) REVERT: J 47 LEU cc_start: 0.7636 (tp) cc_final: 0.7271 (mm) REVERT: L 57 HIS cc_start: 0.7561 (m90) cc_final: 0.7335 (m-70) REVERT: L 169 GLN cc_start: 0.8292 (tp-100) cc_final: 0.8078 (tp-100) outliers start: 61 outliers final: 45 residues processed: 290 average time/residue: 0.1178 time to fit residues: 55.5216 Evaluate side-chains 271 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 TYR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 156 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 52 optimal weight: 0.0050 chunk 232 optimal weight: 0.6980 chunk 202 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN E 205 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.214817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158481 restraints weight = 26407.026| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.91 r_work: 0.3771 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20610 Z= 0.134 Angle : 0.579 11.365 28062 Z= 0.301 Chirality : 0.046 0.233 3144 Planarity : 0.004 0.073 3594 Dihedral : 4.795 23.854 2646 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.62 % Allowed : 15.45 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2514 helix: -1.67 (0.29), residues: 242 sheet: -0.54 (0.15), residues: 1094 loop : -0.22 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 18 TYR 0.017 0.001 TYR K 174 PHE 0.018 0.002 PHE G 157 TRP 0.010 0.001 TRP D 39 HIS 0.003 0.000 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00319 (20580) covalent geometry : angle 0.57854 (28002) SS BOND : bond 0.00402 ( 30) SS BOND : angle 0.78997 ( 60) hydrogen bonds : bond 0.03517 ( 694) hydrogen bonds : angle 5.88891 ( 2109) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 245 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 ASP cc_start: 0.7986 (m-30) cc_final: 0.7559 (p0) REVERT: C 49 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: B 73 GLU cc_start: 0.7230 (mp0) cc_final: 0.7020 (mp0) REVERT: A 71 CYS cc_start: 0.6136 (m) cc_final: 0.5682 (m) REVERT: A 209 ASP cc_start: 0.8078 (p0) cc_final: 0.7833 (p0) REVERT: E 5 TYR cc_start: 0.4435 (OUTLIER) cc_final: 0.3821 (m-80) REVERT: F 99 PHE cc_start: 0.6727 (p90) cc_final: 0.6495 (p90) REVERT: F 126 MET cc_start: 0.7006 (mpp) cc_final: 0.6439 (tmm) REVERT: H 17 SER cc_start: 0.7077 (OUTLIER) cc_final: 0.6747 (p) REVERT: H 68 LEU cc_start: 0.6683 (tp) cc_final: 0.6306 (tp) REVERT: J 29 MET cc_start: 0.5922 (ttm) cc_final: 0.5544 (tpp) REVERT: J 47 LEU cc_start: 0.7660 (tp) cc_final: 0.7303 (mm) outliers start: 60 outliers final: 45 residues processed: 289 average time/residue: 0.1304 time to fit residues: 61.4169 Evaluate side-chains 270 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 TYR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 163 MET Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 103 optimal weight: 0.6980 chunk 233 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN E 205 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 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 = 0.4557 r_free = 0.4557 target = 0.214725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159582 restraints weight = 26400.158| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.39 r_work: 0.3755 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20610 Z= 0.135 Angle : 0.571 9.122 28062 Z= 0.297 Chirality : 0.046 0.234 3144 Planarity : 0.005 0.075 3594 Dihedral : 4.747 23.995 2646 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.84 % Allowed : 16.45 % Favored : 80.72 % 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: -0.83 (0.17), residues: 2514 helix: -1.64 (0.30), residues: 242 sheet: -0.49 (0.15), residues: 1088 loop : -0.16 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 41 TYR 0.019 0.001 TYR H 112 PHE 0.018 0.002 PHE H 16 TRP 0.014 0.001 TRP F 39 HIS 0.003 0.000 HIS L 57 Details of bonding type rmsd covalent geometry : bond 0.00321 (20580) covalent geometry : angle 0.57079 (28002) SS BOND : bond 0.00386 ( 30) SS BOND : angle 0.69604 ( 60) hydrogen bonds : bond 0.03404 ( 694) hydrogen bonds : angle 5.73272 ( 2109) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6427 (m-80) REVERT: A 71 CYS cc_start: 0.5980 (m) cc_final: 0.5558 (m) REVERT: A 209 ASP cc_start: 0.8054 (p0) cc_final: 0.7826 (p0) REVERT: E 5 TYR cc_start: 0.4442 (OUTLIER) cc_final: 0.3807 (m-80) REVERT: F 126 MET cc_start: 0.6925 (mpp) cc_final: 0.6338 (tmm) REVERT: G 123 GLN cc_start: 0.7762 (pp30) cc_final: 0.7267 (mt0) REVERT: H 17 SER cc_start: 0.7118 (OUTLIER) cc_final: 0.6760 (p) REVERT: H 68 LEU cc_start: 0.6790 (tp) cc_final: 0.6406 (tp) REVERT: J 29 MET cc_start: 0.5877 (ttm) cc_final: 0.5525 (tpp) REVERT: J 47 LEU cc_start: 0.7658 (tp) cc_final: 0.7311 (mm) outliers start: 65 outliers final: 52 residues processed: 286 average time/residue: 0.1219 time to fit residues: 56.6737 Evaluate side-chains 283 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 TYR Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 163 MET Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 91 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 171 optimal weight: 20.0000 chunk 192 optimal weight: 0.0040 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS D 102 ASN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** 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 = 0.4565 r_free = 0.4565 target = 0.215532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.160794 restraints weight = 26461.941| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.44 r_work: 0.3806 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20610 Z= 0.123 Angle : 0.567 9.313 28062 Z= 0.294 Chirality : 0.046 0.213 3144 Planarity : 0.004 0.076 3594 Dihedral : 4.675 23.254 2646 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.88 % Allowed : 16.93 % Favored : 80.19 % 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: -0.76 (0.17), residues: 2514 helix: -1.61 (0.30), residues: 242 sheet: -0.42 (0.15), residues: 1088 loop : -0.13 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 41 TYR 0.016 0.001 TYR K 174 PHE 0.020 0.002 PHE G 99 TRP 0.017 0.001 TRP L 39 HIS 0.005 0.000 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00291 (20580) covalent geometry : angle 0.56729 (28002) SS BOND : bond 0.00367 ( 30) SS BOND : angle 0.64793 ( 60) hydrogen bonds : bond 0.03293 ( 694) hydrogen bonds : angle 5.56503 ( 2109) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 241 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 ASP cc_start: 0.7962 (m-30) cc_final: 0.7540 (p0) REVERT: A 209 ASP cc_start: 0.8004 (p0) cc_final: 0.7754 (p0) REVERT: E 5 TYR cc_start: 0.4204 (OUTLIER) cc_final: 0.3550 (m-80) REVERT: F 126 MET cc_start: 0.6909 (mpp) cc_final: 0.6332 (tmm) REVERT: H 17 SER cc_start: 0.6965 (OUTLIER) cc_final: 0.6520 (p) REVERT: H 68 LEU cc_start: 0.6758 (tp) cc_final: 0.6382 (tp) REVERT: J 29 MET cc_start: 0.5697 (ttm) cc_final: 0.5417 (tpp) REVERT: J 47 LEU cc_start: 0.7689 (tp) cc_final: 0.7341 (mm) REVERT: L 48 GLU cc_start: 0.7063 (mp0) cc_final: 0.6821 (mp0) outliers start: 66 outliers final: 55 residues processed: 294 average time/residue: 0.1257 time to fit residues: 60.9758 Evaluate side-chains 289 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 TYR Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 163 MET Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 173 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 71 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS D 102 ASN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN K 205 GLN L 169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.212433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156699 restraints weight = 26452.626| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.67 r_work: 0.3715 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20610 Z= 0.200 Angle : 0.627 10.148 28062 Z= 0.324 Chirality : 0.048 0.292 3144 Planarity : 0.005 0.080 3594 Dihedral : 4.919 26.680 2646 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.01 % Allowed : 17.28 % Favored : 79.71 % 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: -0.83 (0.17), residues: 2514 helix: -1.58 (0.30), residues: 242 sheet: -0.47 (0.15), residues: 1088 loop : -0.19 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 41 TYR 0.024 0.002 TYR H 112 PHE 0.033 0.002 PHE G 157 TRP 0.016 0.001 TRP D 39 HIS 0.006 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00483 (20580) covalent geometry : angle 0.62706 (28002) SS BOND : bond 0.00487 ( 30) SS BOND : angle 0.70286 ( 60) hydrogen bonds : bond 0.03424 ( 694) hydrogen bonds : angle 5.68343 ( 2109) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: C 49 PHE cc_start: 0.7481 (m-80) cc_final: 0.6772 (m-10) REVERT: A 209 ASP cc_start: 0.7996 (p0) cc_final: 0.7732 (p0) REVERT: E 5 TYR cc_start: 0.4209 (OUTLIER) cc_final: 0.3579 (m-80) REVERT: F 126 MET cc_start: 0.6990 (mpp) cc_final: 0.6344 (tmm) REVERT: H 17 SER cc_start: 0.7021 (OUTLIER) cc_final: 0.6558 (p) REVERT: H 68 LEU cc_start: 0.6782 (tp) cc_final: 0.6399 (tp) REVERT: I 171 TYR cc_start: 0.8658 (m-80) cc_final: 0.7621 (m-80) REVERT: J 29 MET cc_start: 0.5815 (ttm) cc_final: 0.5454 (tpp) REVERT: J 47 LEU cc_start: 0.7565 (tp) cc_final: 0.7225 (mm) REVERT: J 126 MET cc_start: 0.4905 (OUTLIER) cc_final: 0.4703 (tpt) REVERT: L 48 GLU cc_start: 0.7119 (mp0) cc_final: 0.6884 (mp0) outliers start: 69 outliers final: 57 residues processed: 284 average time/residue: 0.1174 time to fit residues: 55.0990 Evaluate side-chains 279 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 TYR Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain K residue 49 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 163 MET Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 173 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 173 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 174 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 177 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 169 GLN J 119 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.213873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155628 restraints weight = 26262.872| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.92 r_work: 0.3739 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20610 Z= 0.159 Angle : 0.604 10.661 28062 Z= 0.313 Chirality : 0.047 0.273 3144 Planarity : 0.005 0.080 3594 Dihedral : 4.847 25.318 2646 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.92 % Allowed : 17.80 % Favored : 79.28 % 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: -0.81 (0.17), residues: 2514 helix: -1.56 (0.30), residues: 242 sheet: -0.42 (0.15), residues: 1100 loop : -0.22 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 41 TYR 0.017 0.001 TYR E 112 PHE 0.036 0.002 PHE B 49 TRP 0.017 0.001 TRP D 39 HIS 0.002 0.000 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00382 (20580) covalent geometry : angle 0.60370 (28002) SS BOND : bond 0.00404 ( 30) SS BOND : angle 0.63002 ( 60) hydrogen bonds : bond 0.03291 ( 694) hydrogen bonds : angle 5.56464 ( 2109) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 233 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 GLU cc_start: 0.6967 (mp0) cc_final: 0.6244 (tt0) REVERT: A 209 ASP cc_start: 0.7957 (p0) cc_final: 0.7714 (p0) REVERT: E 5 TYR cc_start: 0.4299 (OUTLIER) cc_final: 0.3588 (m-80) REVERT: F 126 MET cc_start: 0.6947 (mpp) cc_final: 0.6311 (tmm) REVERT: F 202 TYR cc_start: 0.8490 (m-80) cc_final: 0.8054 (m-80) REVERT: H 17 SER cc_start: 0.6829 (OUTLIER) cc_final: 0.6362 (p) REVERT: H 68 LEU cc_start: 0.6691 (tp) cc_final: 0.6299 (tp) REVERT: J 29 MET cc_start: 0.5913 (ttm) cc_final: 0.5455 (tpp) REVERT: J 47 LEU cc_start: 0.7571 (tp) cc_final: 0.7238 (mm) REVERT: J 126 MET cc_start: 0.4891 (OUTLIER) cc_final: 0.4686 (tpt) REVERT: L 48 GLU cc_start: 0.7075 (mp0) cc_final: 0.6861 (mp0) outliers start: 67 outliers final: 58 residues processed: 285 average time/residue: 0.1158 time to fit residues: 54.6105 Evaluate side-chains 286 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 TYR Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 119 GLN Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain K residue 49 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 163 MET Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 121 LEU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 115 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 0.0270 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS D 124 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 GLN K 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.209732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150661 restraints weight = 26409.871| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.76 r_work: 0.3693 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 20610 Z= 0.283 Angle : 0.696 10.233 28062 Z= 0.360 Chirality : 0.051 0.342 3144 Planarity : 0.005 0.085 3594 Dihedral : 5.138 29.969 2646 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.88 % Allowed : 18.11 % Favored : 79.01 % 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: -0.99 (0.17), residues: 2514 helix: -1.63 (0.30), residues: 242 sheet: -0.53 (0.16), residues: 1036 loop : -0.39 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 18 TYR 0.024 0.002 TYR K 174 PHE 0.035 0.003 PHE G 157 TRP 0.025 0.001 TRP D 39 HIS 0.008 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00690 (20580) covalent geometry : angle 0.69565 (28002) SS BOND : bond 0.00622 ( 30) SS BOND : angle 0.79005 ( 60) hydrogen bonds : bond 0.03643 ( 694) hydrogen bonds : angle 5.78576 ( 2109) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 233 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: B 13 ASP cc_start: 0.8226 (m-30) cc_final: 0.7780 (m-30) REVERT: B 86 ARG cc_start: 0.6228 (ttp-110) cc_final: 0.4685 (tpp-160) REVERT: A 209 ASP cc_start: 0.8035 (p0) cc_final: 0.7769 (p0) REVERT: E 5 TYR cc_start: 0.4315 (OUTLIER) cc_final: 0.3629 (m-80) REVERT: E 14 LEU cc_start: 0.8014 (mt) cc_final: 0.7645 (mt) REVERT: F 126 MET cc_start: 0.7036 (mpp) cc_final: 0.6387 (tmm) REVERT: F 202 TYR cc_start: 0.8561 (m-80) cc_final: 0.8127 (m-80) REVERT: H 17 SER cc_start: 0.6900 (OUTLIER) cc_final: 0.6431 (p) REVERT: H 68 LEU cc_start: 0.6827 (tp) cc_final: 0.6432 (tp) REVERT: J 29 MET cc_start: 0.5799 (ttm) cc_final: 0.5540 (tpp) REVERT: J 47 LEU cc_start: 0.7620 (tp) cc_final: 0.7089 (mm) REVERT: J 126 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4859 (tpt) REVERT: L 48 GLU cc_start: 0.7148 (mp0) cc_final: 0.6933 (mp0) outliers start: 66 outliers final: 56 residues processed: 283 average time/residue: 0.1191 time to fit residues: 54.7894 Evaluate side-chains 283 residues out of total 2292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 224 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain D residue 71 CYS Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 5 TYR Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 126 MET Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 150 VAL Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain K residue 49 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 163 MET Chi-restraints excluded: chain K residue 193 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 173 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 236 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 66 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 244 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.213524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.158204 restraints weight = 26548.231| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.24 r_work: 0.3794 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20610 Z= 0.146 Angle : 0.613 10.573 28062 Z= 0.318 Chirality : 0.047 0.282 3144 Planarity : 0.005 0.081 3594 Dihedral : 4.927 25.601 2646 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.62 % Allowed : 18.67 % Favored : 78.71 % 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: -0.82 (0.17), residues: 2514 helix: -1.62 (0.30), residues: 242 sheet: -0.44 (0.16), residues: 1022 loop : -0.24 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 41 TYR 0.022 0.001 TYR H 112 PHE 0.032 0.002 PHE B 49 TRP 0.021 0.001 TRP D 39 HIS 0.002 0.000 HIS J 196 Details of bonding type rmsd covalent geometry : bond 0.00352 (20580) covalent geometry : angle 0.61278 (28002) SS BOND : bond 0.00375 ( 30) SS BOND : angle 0.63564 ( 60) hydrogen bonds : bond 0.03284 ( 694) hydrogen bonds : angle 5.52453 ( 2109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4609.95 seconds wall clock time: 79 minutes 52.52 seconds (4792.52 seconds total)