Starting phenix.real_space_refine on Fri Jul 3 12:52:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dul_27722/07_2026/8dul_27722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dul_27722/07_2026/8dul_27722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dul_27722/07_2026/8dul_27722.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dul_27722/07_2026/8dul_27722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dul_27722/07_2026/8dul_27722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dul_27722/07_2026/8dul_27722.map" model { file = "/net/cci-nas-00/data/ceres_data/8dul_27722/07_2026/8dul_27722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dul_27722/07_2026/8dul_27722.cif" } resolution = 4.17 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= -0.000 sd= 0.032 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 95 5.16 5 C 8978 2.51 5 N 2444 2.21 5 O 2686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14203 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2597 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 20, 'TRANS': 308} Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1407 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 168} Chain breaks: 1 Chain: "G" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2597 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 20, 'TRANS': 308} Chain: "J" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1508 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 181} Chain breaks: 1 Chain: "K" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2631 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1535 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 185} Chain breaks: 1 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 975 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.81, per 1000 atoms: 0.20 Number of scatterers: 14203 At special positions: 0 Unit cell: (141.1, 119.52, 131.14, 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 95 16.00 O 2686 8.00 N 2444 7.00 C 8978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 204 " - pdb=" SG CYS B 229 " distance=2.04 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.03 Simple disulfide: pdb=" SG CYS G 94 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 269 " distance=2.02 Simple disulfide: pdb=" SG CYS G 204 " - pdb=" SG CYS G 229 " distance=2.03 Simple disulfide: pdb=" SG CYS G 206 " - pdb=" SG CYS G 223 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.02 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 127 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 28 " distance=2.03 Simple disulfide: pdb=" SG CYS K 94 " - pdb=" SG CYS K 108 " distance=2.03 Simple disulfide: pdb=" SG CYS K 155 " - pdb=" SG CYS K 269 " distance=2.03 Simple disulfide: pdb=" SG CYS K 204 " - pdb=" SG CYS K 229 " distance=2.03 Simple disulfide: pdb=" SG CYS K 206 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A3001 " - " ASN A 245 " " NAG B 501 " - " ASN B 321 " " NAG B 502 " - " ASN B 199 " " NAG C 1 " - " ASN K 321 " " NAG F3001 " - " ASN F 245 " " NAG G 501 " - " ASN G 321 " " NAG G 502 " - " ASN G 199 " " NAG J3001 " - " ASN J 245 " " NAG K 501 " - " ASN K 199 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 613.5 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 50 sheets defined 2.6% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'F' and resid 112 through 116 removed outlier: 4.257A pdb=" N THR F 115 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE F 116 " --> pdb=" O ASP F 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 112 through 116' Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.701A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.631A pdb=" N GLY B 17 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.658A pdb=" N TRP B 38 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR B 102 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE B 88 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ARG B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N ILE B 86 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 114 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 129 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 116 " --> pdb=" O CYS B 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 70 Processing sheet with id=AA4, first strand: chain 'B' and resid 151 through 158 removed outlier: 3.545A pdb=" N LYS B 151 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 183 through 186 removed outlier: 3.504A pdb=" N ALA B 186 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 214 removed outlier: 4.469A pdb=" N SER B 210 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS B 204 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 212 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 230 " --> pdb=" O GLU B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 282 removed outlier: 3.545A pdb=" N LEU B 290 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 318 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 310 through 314 removed outlier: 3.563A pdb=" N ILE B 314 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 48 removed outlier: 6.189A pdb=" N LYS A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS A 123 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.803A pdb=" N VAL A 54 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.803A pdb=" N VAL A 54 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AB5, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AB6, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AB7, first strand: chain 'G' and resid 34 through 38 removed outlier: 7.127A pdb=" N GLN G 49 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL G 37 " --> pdb=" O ARG G 47 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG G 47 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N ILE G 48 " --> pdb=" O GLN G 107 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N GLN G 107 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 11.164A pdb=" N VAL G 50 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N LEU G 105 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N ALA G 52 " --> pdb=" O PHE G 103 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE G 103 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE G 88 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ARG G 96 " --> pdb=" O ILE G 86 " (cutoff:3.500A) removed outlier: 11.386A pdb=" N ILE G 86 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.733A pdb=" N ASP G 81 " --> pdb=" O PHE G 67 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR G 69 " --> pdb=" O LYS G 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 151 through 158 removed outlier: 3.639A pdb=" N LYS G 151 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL G 271 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS G 155 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR G 267 " --> pdb=" O CYS G 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 240 through 241 removed outlier: 3.720A pdb=" N GLY G 167 " --> pdb=" O ILE G 260 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 183 through 186 removed outlier: 4.491A pdb=" N VAL G 190 " --> pdb=" O MET G 220 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET G 220 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 209 through 214 removed outlier: 3.502A pdb=" N SER G 210 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 212 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR G 202 " --> pdb=" O GLY G 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 278 through 282 Processing sheet with id=AC5, first strand: chain 'G' and resid 310 through 314 removed outlier: 3.842A pdb=" N TYR G 331 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 339 " --> pdb=" O TYR G 331 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'J' and resid 43 through 48 removed outlier: 6.345A pdb=" N LYS J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LYS J 123 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.544A pdb=" N VAL J 54 " --> pdb=" O TYR J 107 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR J 107 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN J 59 " --> pdb=" O LEU J 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 51 through 54 removed outlier: 3.544A pdb=" N VAL J 54 " --> pdb=" O TYR J 107 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR J 107 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN J 102 " --> pdb=" O VAL J 80 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N VAL J 80 " --> pdb=" O GLN J 102 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER J 104 " --> pdb=" O CYS J 78 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N CYS J 78 " --> pdb=" O SER J 104 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA J 106 " --> pdb=" O TYR J 76 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR J 76 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA J 74 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AD2, first strand: chain 'J' and resid 220 through 221 removed outlier: 3.709A pdb=" N ARG J 220 " --> pdb=" O THR J 234 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AD4, first strand: chain 'K' and resid 34 through 38 removed outlier: 8.172A pdb=" N ILE K 34 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER K 51 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN K 36 " --> pdb=" O GLN K 49 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN K 49 " --> pdb=" O ASN K 36 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N ILE K 48 " --> pdb=" O GLN K 107 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N GLN K 107 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N VAL K 50 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N LEU K 105 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ALA K 52 " --> pdb=" O PHE K 103 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE K 103 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE K 88 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ARG K 96 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N ILE K 86 " --> pdb=" O ARG K 96 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL K 114 " --> pdb=" O VAL K 129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 66 through 70 Processing sheet with id=AD6, first strand: chain 'K' and resid 151 through 158 removed outlier: 3.508A pdb=" N LYS K 151 " --> pdb=" O VAL K 271 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 240 through 241 removed outlier: 3.643A pdb=" N MET K 171 " --> pdb=" O GLY K 256 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY K 256 " --> pdb=" O MET K 171 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 183 through 186 removed outlier: 4.438A pdb=" N VAL K 190 " --> pdb=" O MET K 220 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET K 220 " --> pdb=" O VAL K 190 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 209 through 214 Processing sheet with id=AE1, first strand: chain 'K' and resid 278 through 282 removed outlier: 3.637A pdb=" N GLY K 285 " --> pdb=" O TRP K 282 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG K 294 " --> pdb=" O ILE K 314 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE K 314 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR K 296 " --> pdb=" O GLU K 312 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU K 312 " --> pdb=" O THR K 296 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU K 298 " --> pdb=" O THR K 310 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR K 310 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 278 through 282 removed outlier: 3.637A pdb=" N GLY K 285 " --> pdb=" O TRP K 282 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 37 through 38 removed outlier: 4.052A pdb=" N LYS F 260 " --> pdb=" O SER F 269 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 42 through 48 removed outlier: 6.094A pdb=" N LYS F 44 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS F 123 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL F 177 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.668A pdb=" N HIS F 52 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 109 " --> pdb=" O HIS F 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 54 " --> pdb=" O TYR F 107 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR F 107 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA F 106 " --> pdb=" O TYR F 76 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR F 76 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA F 74 " --> pdb=" O VAL F 108 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 59 through 60 Processing sheet with id=AE7, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AE8, first strand: chain 'F' and resid 220 through 221 removed outlier: 4.056A pdb=" N ARG F 220 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.029A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP H 72 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.827A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 97 through 100A removed outlier: 3.904A pdb=" N SER H 99 " --> pdb=" O TYR H 100F" (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 19 through 22 removed outlier: 4.465A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 53 through 54 removed outlier: 4.002A pdb=" N GLU L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR L 49 " --> pdb=" O GLU L 53 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARG L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 861 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: 2.15 Time building geometry restraints manager: 1.49 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: 4518 1.34 - 1.47: 3619 1.47 - 1.59: 6324 1.59 - 1.72: 0 1.72 - 1.84: 119 Bond restraints: 14580 Sorted by residual: bond pdb=" C LYS B 193 " pdb=" N PRO B 194 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.35e+00 bond pdb=" N LYS B 193 " pdb=" CA LYS B 193 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.10e-02 8.26e+03 7.15e+00 bond pdb=" N VAL B 200 " pdb=" CA VAL B 200 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.29e-02 6.01e+03 6.48e+00 bond pdb=" N VAL K 200 " pdb=" CA VAL K 200 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.29e-02 6.01e+03 6.23e+00 bond pdb=" N ASN A 246 " pdb=" CA ASN A 246 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.16e-02 7.43e+03 6.18e+00 ... (remaining 14575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 19481 3.43 - 6.86: 258 6.86 - 10.30: 43 10.30 - 13.73: 1 13.73 - 17.16: 1 Bond angle restraints: 19784 Sorted by residual: angle pdb=" CA GLU J 99 " pdb=" CB GLU J 99 " pdb=" CG GLU J 99 " ideal model delta sigma weight residual 114.10 126.53 -12.43 2.00e+00 2.50e-01 3.87e+01 angle pdb=" O LYS B 281 " pdb=" C LYS B 281 " pdb=" N TRP B 282 " ideal model delta sigma weight residual 123.27 129.07 -5.80 1.13e+00 7.83e-01 2.64e+01 angle pdb=" CA LEU F 221 " pdb=" CB LEU F 221 " pdb=" CG LEU F 221 " ideal model delta sigma weight residual 116.30 133.46 -17.16 3.50e+00 8.16e-02 2.40e+01 angle pdb=" CA LYS B 281 " pdb=" C LYS B 281 " pdb=" N TRP B 282 " ideal model delta sigma weight residual 116.25 110.39 5.86 1.23e+00 6.61e-01 2.27e+01 angle pdb=" C CYS J 62 " pdb=" CA CYS J 62 " pdb=" CB CYS J 62 " ideal model delta sigma weight residual 110.88 103.59 7.29 1.57e+00 4.06e-01 2.15e+01 ... (remaining 19779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 7892 17.67 - 35.34: 647 35.34 - 53.00: 123 53.00 - 70.67: 12 70.67 - 88.34: 12 Dihedral angle restraints: 8686 sinusoidal: 3476 harmonic: 5210 Sorted by residual: dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual 93.00 144.68 -51.68 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CA CYS G 22 " pdb=" C CYS G 22 " pdb=" N ARG G 23 " pdb=" CA ARG G 23 " ideal model delta harmonic sigma weight residual -180.00 -150.39 -29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA HIS G 99 " pdb=" C HIS G 99 " pdb=" N LYS G 100 " pdb=" CA LYS G 100 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 8683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 2153 0.237 - 0.473: 16 0.473 - 0.710: 1 0.710 - 0.947: 0 0.947 - 1.184: 1 Chirality restraints: 2171 Sorted by residual: chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 321 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-01 2.50e+01 3.50e+01 chirality pdb=" C1 NAG F3001 " pdb=" ND2 ASN F 245 " pdb=" C2 NAG F3001 " pdb=" O5 NAG F3001 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" C1 NAG K 501 " pdb=" ND2 ASN K 199 " pdb=" C2 NAG K 501 " pdb=" O5 NAG K 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 ... (remaining 2168 not shown) Planarity restraints: 2534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG B 502 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " 0.095 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.535 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 501 " 0.329 2.00e-02 2.50e+03 2.81e-01 9.87e+02 pdb=" C7 NAG K 501 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG K 501 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG K 501 " -0.493 2.00e-02 2.50e+03 pdb=" O7 NAG K 501 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.320 2.00e-02 2.50e+03 2.70e-01 9.11e+02 pdb=" C7 NAG C 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.191 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.466 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.038 2.00e-02 2.50e+03 ... (remaining 2531 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4349 2.83 - 3.35: 11764 3.35 - 3.87: 23590 3.87 - 4.38: 25226 4.38 - 4.90: 43987 Nonbonded interactions: 108916 Sorted by model distance: nonbonded pdb=" OG SER G 71 " pdb=" OD2 ASP G 73 " model vdw 2.317 3.040 nonbonded pdb=" OG SER H 35 " pdb=" OD2 ASP H 95 " model vdw 2.319 3.040 nonbonded pdb=" OG SER K 89 " pdb=" OG1 THR K 115 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLU B 203 " pdb=" OG1 THR B 211 " model vdw 2.332 3.040 nonbonded pdb=" OD1 ASP L 50 " pdb=" OH TYR L 91 " model vdw 2.339 3.040 ... (remaining 108911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'F' and (resid 42 through 124 or resid 171 through 268 or resid 3001)) selection = (chain 'J' and (resid 42 through 124 or resid 171 through 268 or resid 3001)) } ncs_group { reference = (chain 'B' and (resid 14 through 342 or resid 502)) selection = (chain 'G' and (resid 14 through 342 or resid 502)) selection = (chain 'K' and (resid 14 through 342 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.190 Find NCS groups from input model: 0.290 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4911 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 : 0.005 0.080 14622 Z= 0.261 Angle : 1.059 17.160 19878 Z= 0.574 Chirality : 0.071 1.184 2171 Planarity : 0.016 0.301 2525 Dihedral : 13.223 88.339 5254 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.06 % Allowed : 0.71 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -2.03 (0.18), residues: 1780 helix: -2.04 (0.69), residues: 43 sheet: -0.78 (0.21), residues: 553 loop : -1.68 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG G 23 TYR 0.043 0.002 TYR A 85 PHE 0.037 0.003 PHE B 18 TRP 0.033 0.002 TRP B 282 HIS 0.015 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.26 (14580) covalent geometry : angle 1.04376 / 0.57 (19784) SS BOND : bond 0.00430 / 0.19 ( 32) SS BOND : angle 1.43959 / 0.82 ( 64) hydrogen bonds : bond 0.28484 / 18.54 ( 336) hydrogen bonds : angle 10.36012 / 6.99 ( 861) link_BETA1-4 : bond 0.00660 / 0.44 ( 1) link_BETA1-4 : angle 1.50224 / 1.03 ( 3) link_NAG-ASN : bond 0.00526 / 0.33 ( 9) link_NAG-ASN : angle 4.73238 / 3.62 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7750 (mpp) cc_final: 0.7040 (mpp) REVERT: B 228 GLN cc_start: 0.7630 (mt0) cc_final: 0.7258 (mt0) REVERT: G 68 ARG cc_start: 0.5032 (mmt180) cc_final: 0.4641 (mmt180) REVERT: G 81 ASP cc_start: 0.5771 (m-30) cc_final: 0.5470 (m-30) REVERT: G 235 ASP cc_start: 0.7655 (m-30) cc_final: 0.7249 (m-30) REVERT: J 115 THR cc_start: 0.8168 (p) cc_final: 0.7880 (p) REVERT: K 56 TYR cc_start: 0.7335 (m-80) cc_final: 0.7059 (m-10) REVERT: K 220 MET cc_start: 0.0999 (ttt) cc_final: 0.0694 (tpt) REVERT: F 103 LEU cc_start: 0.7476 (tp) cc_final: 0.6903 (tt) REVERT: F 113 ASP cc_start: 0.5198 (p0) cc_final: 0.3981 (p0) REVERT: F 209 ASP cc_start: 0.6385 (p0) cc_final: 0.6143 (p0) REVERT: H 100 VAL cc_start: 0.3308 (m) cc_final: 0.2454 (m) outliers start: 1 outliers final: 1 residues processed: 459 average time/residue: 0.1128 time to fit residues: 74.0350 Evaluate side-chains 273 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS B 255 GLN B 259 HIS ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN A 246 ASN G 177 HIS G 242 ASN J 125 HIS ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.143241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.122680 restraints weight = 60039.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.125880 restraints weight = 40438.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.127921 restraints weight = 27045.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.128628 restraints weight = 21130.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.129242 restraints weight = 17191.420| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6431 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14622 Z= 0.172 Angle : 0.682 8.262 19878 Z= 0.353 Chirality : 0.046 0.227 2171 Planarity : 0.006 0.059 2525 Dihedral : 5.306 21.420 1962 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.63 (0.18), residues: 1780 helix: -1.47 (0.71), residues: 45 sheet: -0.48 (0.22), residues: 519 loop : -1.41 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 50 TYR 0.017 0.002 TYR K 168 PHE 0.017 0.002 PHE A 95 TRP 0.028 0.002 TRP F 243 HIS 0.009 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (14580) covalent geometry : angle 0.67376 / 0.35 (19784) SS BOND : bond 0.00427 / 0.21 ( 32) SS BOND : angle 1.06788 / 0.66 ( 64) hydrogen bonds : bond 0.04677 / 3.08 ( 336) hydrogen bonds : angle 7.10071 / 4.85 ( 861) link_BETA1-4 : bond 0.00106 / 0.07 ( 1) link_BETA1-4 : angle 1.20192 / 0.67 ( 3) link_NAG-ASN : bond 0.00751 / 0.35 ( 9) link_NAG-ASN : angle 2.68549 / 1.64 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7079 (mpp) cc_final: 0.6427 (mpp) REVERT: B 81 ASP cc_start: 0.7735 (t0) cc_final: 0.7390 (t0) REVERT: B 105 LEU cc_start: 0.7352 (tt) cc_final: 0.7065 (tp) REVERT: B 107 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8013 (mm-40) REVERT: A 97 ASP cc_start: 0.8333 (p0) cc_final: 0.7694 (p0) REVERT: A 118 HIS cc_start: 0.9358 (p-80) cc_final: 0.8954 (p-80) REVERT: A 217 THR cc_start: 0.8698 (p) cc_final: 0.8444 (p) REVERT: A 219 ILE cc_start: 0.8954 (tp) cc_final: 0.8508 (tp) REVERT: A 220 ARG cc_start: 0.8126 (mpp80) cc_final: 0.7550 (ptt-90) REVERT: G 38 TRP cc_start: 0.8821 (m-90) cc_final: 0.8406 (m-90) REVERT: G 64 VAL cc_start: 0.8581 (p) cc_final: 0.8252 (p) REVERT: G 81 ASP cc_start: 0.7584 (m-30) cc_final: 0.7255 (m-30) REVERT: G 95 ARG cc_start: 0.8452 (tmm-80) cc_final: 0.8115 (tmm-80) REVERT: G 235 ASP cc_start: 0.7674 (m-30) cc_final: 0.7460 (m-30) REVERT: J 99 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7932 (pt0) REVERT: J 233 TYR cc_start: 0.8518 (p90) cc_final: 0.8117 (p90) REVERT: K 38 TRP cc_start: 0.8643 (m-90) cc_final: 0.8270 (m-90) REVERT: K 89 SER cc_start: 0.8465 (p) cc_final: 0.8263 (m) REVERT: K 220 MET cc_start: 0.4155 (ttt) cc_final: 0.3501 (tpt) REVERT: K 235 ASP cc_start: 0.7971 (t0) cc_final: 0.7572 (t0) REVERT: K 241 PHE cc_start: 0.8476 (t80) cc_final: 0.8113 (t80) REVERT: K 262 PHE cc_start: 0.7207 (m-80) cc_final: 0.5806 (m-10) REVERT: K 289 HIS cc_start: 0.8644 (m-70) cc_final: 0.8281 (m-70) REVERT: K 336 HIS cc_start: 0.6365 (m90) cc_final: 0.5828 (m-70) REVERT: F 51 PHE cc_start: 0.8159 (p90) cc_final: 0.7436 (p90) REVERT: F 103 LEU cc_start: 0.8273 (tp) cc_final: 0.7917 (tt) REVERT: F 233 TYR cc_start: 0.8640 (p90) cc_final: 0.7668 (p90) REVERT: F 242 MET cc_start: 0.9466 (tpp) cc_final: 0.9215 (tpp) REVERT: H 66 ARG cc_start: -0.1774 (mmt180) cc_final: -0.2818 (mmm160) REVERT: H 96 ASP cc_start: 0.8423 (p0) cc_final: 0.8097 (p0) REVERT: L 3 GLN cc_start: 0.3857 (tt0) cc_final: 0.3514 (tt0) REVERT: L 5 THR cc_start: 0.8048 (p) cc_final: 0.7835 (p) REVERT: L 45 LYS cc_start: 0.8601 (tptp) cc_final: 0.8281 (tppt) REVERT: L 69 THR cc_start: 0.7706 (m) cc_final: 0.7390 (t) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1242 time to fit residues: 62.6077 Evaluate side-chains 243 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 107 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.0070 chunk 47 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 GLN J 230 HIS K 99 HIS K 125 ASN K 259 HIS F 100 ASN F 102 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.134977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.116238 restraints weight = 58059.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.117230 restraints weight = 41624.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.117973 restraints weight = 32534.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.118260 restraints weight = 26466.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.118819 restraints weight = 23982.382| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 14622 Z= 0.257 Angle : 0.776 12.392 19878 Z= 0.409 Chirality : 0.047 0.202 2171 Planarity : 0.006 0.097 2525 Dihedral : 5.795 32.821 1962 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.52 % Allowed : 6.67 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.72 (0.18), residues: 1780 helix: -1.33 (0.67), residues: 45 sheet: -0.66 (0.20), residues: 602 loop : -1.44 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG J 249 TYR 0.032 0.002 TYR A 46 PHE 0.024 0.003 PHE J 170 TRP 0.021 0.003 TRP F 243 HIS 0.008 0.002 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.26 (14580) covalent geometry : angle 0.76384 / 0.40 (19784) SS BOND : bond 0.00368 / 0.21 ( 32) SS BOND : angle 2.14356 / 1.08 ( 64) hydrogen bonds : bond 0.04346 / 2.87 ( 336) hydrogen bonds : angle 6.97817 / 4.76 ( 861) link_BETA1-4 : bond 0.00388 / 0.26 ( 1) link_BETA1-4 : angle 0.73766 / 0.51 ( 3) link_NAG-ASN : bond 0.00408 / 0.20 ( 9) link_NAG-ASN : angle 2.30858 / 1.47 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 330 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LEU cc_start: 0.8254 (pt) cc_final: 0.7952 (tt) REVERT: B 36 ASN cc_start: 0.8647 (t0) cc_final: 0.8025 (t0) REVERT: B 81 ASP cc_start: 0.7803 (t0) cc_final: 0.7481 (t0) REVERT: B 105 LEU cc_start: 0.7792 (tt) cc_final: 0.7471 (tp) REVERT: B 107 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7375 (mm-40) REVERT: B 333 TRP cc_start: 0.8024 (t-100) cc_final: 0.7780 (t-100) REVERT: A 66 LEU cc_start: 0.7743 (mm) cc_final: 0.6946 (mt) REVERT: A 97 ASP cc_start: 0.8305 (p0) cc_final: 0.7705 (p0) REVERT: A 109 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 124 VAL cc_start: 0.7206 (OUTLIER) cc_final: 0.6802 (t) REVERT: A 202 ASP cc_start: 0.8163 (p0) cc_final: 0.7537 (t70) REVERT: A 219 ILE cc_start: 0.9051 (tp) cc_final: 0.8459 (tp) REVERT: A 235 GLN cc_start: 0.8944 (tt0) cc_final: 0.8230 (tt0) REVERT: G 36 ASN cc_start: 0.8829 (t0) cc_final: 0.8364 (t0) REVERT: G 95 ARG cc_start: 0.8542 (tmm-80) cc_final: 0.8277 (tmm-80) REVERT: J 59 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7143 (tm-30) REVERT: J 99 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7986 (pt0) REVERT: J 233 TYR cc_start: 0.8545 (p90) cc_final: 0.8320 (p90) REVERT: J 241 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8378 (mm-30) REVERT: K 70 MET cc_start: 0.9535 (tmm) cc_final: 0.9182 (tmm) REVERT: K 83 MET cc_start: 0.8213 (mmp) cc_final: 0.8002 (mmp) REVERT: K 103 PHE cc_start: 0.8331 (m-10) cc_final: 0.8055 (m-10) REVERT: K 180 LYS cc_start: 0.8726 (ptpp) cc_final: 0.8376 (mtmm) REVERT: K 235 ASP cc_start: 0.7800 (t0) cc_final: 0.7376 (t0) REVERT: K 289 HIS cc_start: 0.9003 (m-70) cc_final: 0.8636 (m-70) REVERT: K 297 LEU cc_start: 0.8943 (tp) cc_final: 0.8290 (tp) REVERT: F 46 TYR cc_start: 0.8169 (p90) cc_final: 0.7736 (p90) REVERT: F 51 PHE cc_start: 0.8473 (p90) cc_final: 0.7510 (p90) REVERT: F 55 ILE cc_start: 0.9398 (mt) cc_final: 0.9167 (mp) REVERT: F 103 LEU cc_start: 0.8440 (tp) cc_final: 0.7778 (tt) REVERT: F 233 TYR cc_start: 0.8659 (p90) cc_final: 0.7392 (p90) REVERT: F 242 MET cc_start: 0.9465 (tpp) cc_final: 0.9254 (tpp) REVERT: H 66 ARG cc_start: -0.0627 (mmt180) cc_final: -0.0919 (mmt90) REVERT: H 100 PHE cc_start: 0.8372 (m-80) cc_final: 0.7973 (m-80) REVERT: L 24 ARG cc_start: 0.3304 (ptt180) cc_final: 0.3099 (ptt-90) REVERT: L 33 LEU cc_start: 0.8920 (tp) cc_final: 0.8719 (tp) REVERT: L 36 TYR cc_start: 0.6249 (m-80) cc_final: 0.5961 (m-80) REVERT: L 69 THR cc_start: 0.7821 (m) cc_final: 0.7411 (t) REVERT: L 73 LEU cc_start: 0.9196 (tp) cc_final: 0.8975 (tp) outliers start: 8 outliers final: 3 residues processed: 336 average time/residue: 0.1244 time to fit residues: 60.3828 Evaluate side-chains 247 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 243 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 75 optimal weight: 0.0170 chunk 1 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.0020 chunk 140 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 255 GLN A 59 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 HIS K 336 HIS F 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.139627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.119103 restraints weight = 60255.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.121550 restraints weight = 45014.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122342 restraints weight = 33888.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.123034 restraints weight = 27192.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.123513 restraints weight = 24554.025| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14622 Z= 0.119 Angle : 0.628 7.468 19878 Z= 0.322 Chirality : 0.046 0.226 2171 Planarity : 0.005 0.069 2525 Dihedral : 5.251 26.070 1962 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.57 (0.18), residues: 1780 helix: -1.21 (0.69), residues: 45 sheet: -0.46 (0.20), residues: 607 loop : -1.41 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 50 TYR 0.019 0.001 TYR B 69 PHE 0.021 0.002 PHE A 95 TRP 0.023 0.002 TRP K 282 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14580) covalent geometry : angle 0.62205 / 0.32 (19784) SS BOND : bond 0.00328 / 0.19 ( 32) SS BOND : angle 1.27246 / 0.87 ( 64) hydrogen bonds : bond 0.03424 / 2.27 ( 336) hydrogen bonds : angle 6.34702 / 4.36 ( 861) link_BETA1-4 : bond 0.00398 / 0.27 ( 1) link_BETA1-4 : angle 1.02445 / 0.64 ( 3) link_NAG-ASN : bond 0.00290 / 0.17 ( 9) link_NAG-ASN : angle 1.55837 / 0.99 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LEU cc_start: 0.8144 (pt) cc_final: 0.7809 (tt) REVERT: B 29 PHE cc_start: 0.9031 (m-10) cc_final: 0.8697 (m-10) REVERT: B 102 TYR cc_start: 0.8243 (m-10) cc_final: 0.7793 (m-10) REVERT: B 105 LEU cc_start: 0.7534 (tt) cc_final: 0.7311 (tp) REVERT: B 107 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7177 (mm-40) REVERT: B 137 PHE cc_start: 0.9031 (p90) cc_final: 0.7711 (p90) REVERT: B 228 GLN cc_start: 0.8415 (mt0) cc_final: 0.8047 (mt0) REVERT: B 230 ILE cc_start: 0.7922 (pt) cc_final: 0.7646 (mt) REVERT: B 333 TRP cc_start: 0.8286 (t-100) cc_final: 0.8023 (t-100) REVERT: A 66 LEU cc_start: 0.7693 (mm) cc_final: 0.6964 (mt) REVERT: A 88 MET cc_start: 0.7764 (ttm) cc_final: 0.7324 (ttt) REVERT: A 97 ASP cc_start: 0.8273 (p0) cc_final: 0.7661 (p0) REVERT: G 36 ASN cc_start: 0.9026 (t0) cc_final: 0.8673 (t0) REVERT: G 38 TRP cc_start: 0.9110 (m-90) cc_final: 0.8274 (m-90) REVERT: G 54 PHE cc_start: 0.8657 (m-80) cc_final: 0.8345 (m-80) REVERT: G 95 ARG cc_start: 0.8370 (tmm-80) cc_final: 0.8123 (tmm-80) REVERT: J 50 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.7529 (ttm-80) REVERT: J 59 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7860 (tm-30) REVERT: J 99 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8098 (pt0) REVERT: J 219 ILE cc_start: 0.8688 (tp) cc_final: 0.8368 (mm) REVERT: J 241 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8077 (mm-30) REVERT: K 70 MET cc_start: 0.9427 (tmm) cc_final: 0.9078 (tmm) REVERT: K 180 LYS cc_start: 0.8714 (ptpp) cc_final: 0.8375 (mtmm) REVERT: K 235 ASP cc_start: 0.7868 (t0) cc_final: 0.7377 (t0) REVERT: K 289 HIS cc_start: 0.8828 (m-70) cc_final: 0.8487 (m-70) REVERT: F 51 PHE cc_start: 0.8270 (p90) cc_final: 0.7449 (p90) REVERT: F 233 TYR cc_start: 0.8424 (p90) cc_final: 0.7255 (p90) REVERT: F 242 MET cc_start: 0.9393 (tpp) cc_final: 0.9174 (tpp) REVERT: H 66 ARG cc_start: -0.1130 (mmt180) cc_final: -0.3109 (mmm-85) REVERT: H 77 THR cc_start: 0.5741 (p) cc_final: 0.5302 (p) REVERT: H 100 PHE cc_start: 0.8238 (m-80) cc_final: 0.7591 (m-80) REVERT: L 5 THR cc_start: 0.8181 (p) cc_final: 0.7717 (p) REVERT: L 69 THR cc_start: 0.7923 (m) cc_final: 0.7543 (t) REVERT: L 76 ASN cc_start: 0.7851 (m110) cc_final: 0.7650 (m110) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1266 time to fit residues: 61.0807 Evaluate side-chains 239 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 65 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 123 optimal weight: 0.0870 chunk 148 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.139812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.119626 restraints weight = 61362.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.121675 restraints weight = 46595.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.122887 restraints weight = 34621.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.123363 restraints weight = 28387.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.124126 restraints weight = 25650.019| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14622 Z= 0.120 Angle : 0.608 7.197 19878 Z= 0.313 Chirality : 0.045 0.206 2171 Planarity : 0.005 0.074 2525 Dihedral : 5.132 31.170 1962 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.46 (0.19), residues: 1780 helix: -1.10 (0.70), residues: 45 sheet: -0.39 (0.20), residues: 618 loop : -1.34 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 50 TYR 0.018 0.001 TYR K 69 PHE 0.040 0.001 PHE G 103 TRP 0.025 0.002 TRP H 103 HIS 0.004 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14580) covalent geometry : angle 0.59983 / 0.31 (19784) SS BOND : bond 0.00613 / 0.25 ( 32) SS BOND : angle 1.34769 / 0.77 ( 64) hydrogen bonds : bond 0.03204 / 2.12 ( 336) hydrogen bonds : angle 6.09824 / 4.19 ( 861) link_BETA1-4 : bond 0.00469 / 0.31 ( 1) link_BETA1-4 : angle 0.88143 / 0.55 ( 3) link_NAG-ASN : bond 0.00510 / 0.18 ( 9) link_NAG-ASN : angle 2.04740 / 1.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LEU cc_start: 0.8114 (pt) cc_final: 0.7745 (tt) REVERT: B 46 ILE cc_start: 0.9559 (pt) cc_final: 0.9353 (mp) REVERT: B 81 ASP cc_start: 0.8107 (t0) cc_final: 0.7747 (t0) REVERT: B 102 TYR cc_start: 0.8235 (m-10) cc_final: 0.7379 (m-10) REVERT: B 105 LEU cc_start: 0.7781 (tt) cc_final: 0.7550 (tp) REVERT: B 228 GLN cc_start: 0.8355 (mt0) cc_final: 0.8043 (mt0) REVERT: B 237 THR cc_start: 0.8581 (t) cc_final: 0.8317 (p) REVERT: B 333 TRP cc_start: 0.8288 (t-100) cc_final: 0.8026 (t-100) REVERT: A 66 LEU cc_start: 0.7462 (mm) cc_final: 0.6723 (mt) REVERT: A 97 ASP cc_start: 0.8302 (p0) cc_final: 0.7669 (p0) REVERT: A 109 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7649 (tm-30) REVERT: G 36 ASN cc_start: 0.8972 (t0) cc_final: 0.8593 (t0) REVERT: G 38 TRP cc_start: 0.8611 (m-90) cc_final: 0.8315 (m-90) REVERT: G 76 HIS cc_start: 0.7539 (p-80) cc_final: 0.7266 (p-80) REVERT: G 77 ASP cc_start: 0.8058 (m-30) cc_final: 0.7259 (p0) REVERT: G 95 ARG cc_start: 0.8473 (tmm-80) cc_final: 0.8025 (tmm-80) REVERT: J 59 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7828 (tm-30) REVERT: J 99 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8113 (pt0) REVERT: J 219 ILE cc_start: 0.8692 (tp) cc_final: 0.8351 (mm) REVERT: J 233 TYR cc_start: 0.8354 (p90) cc_final: 0.7958 (p90) REVERT: K 46 ILE cc_start: 0.9408 (mp) cc_final: 0.9190 (tp) REVERT: K 70 MET cc_start: 0.9465 (tmm) cc_final: 0.9180 (tmm) REVERT: K 180 LYS cc_start: 0.8648 (ptpp) cc_final: 0.8254 (mtmm) REVERT: K 235 ASP cc_start: 0.7929 (t0) cc_final: 0.7395 (t0) REVERT: K 289 HIS cc_start: 0.8846 (m-70) cc_final: 0.8542 (m90) REVERT: F 51 PHE cc_start: 0.8250 (p90) cc_final: 0.7379 (p90) REVERT: F 233 TYR cc_start: 0.8560 (p90) cc_final: 0.7351 (p90) REVERT: F 242 MET cc_start: 0.9438 (tpp) cc_final: 0.9194 (tpp) REVERT: H 36 TRP cc_start: 0.8061 (m-10) cc_final: 0.7438 (m-90) REVERT: H 66 ARG cc_start: -0.1182 (mmt180) cc_final: -0.3121 (mmm-85) REVERT: H 100 PHE cc_start: 0.7173 (m-80) cc_final: 0.6967 (m-10) REVERT: L 45 LYS cc_start: 0.8735 (tptp) cc_final: 0.8304 (tppt) REVERT: L 69 THR cc_start: 0.7957 (m) cc_final: 0.7584 (t) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1309 time to fit residues: 59.5322 Evaluate side-chains 241 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 115 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 160 HIS B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.115433 restraints weight = 60399.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.116809 restraints weight = 44056.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.117742 restraints weight = 36525.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.118132 restraints weight = 28519.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.118655 restraints weight = 27372.756| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14622 Z= 0.190 Angle : 0.671 8.371 19878 Z= 0.344 Chirality : 0.045 0.189 2171 Planarity : 0.005 0.071 2525 Dihedral : 5.419 29.132 1962 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.65 (0.19), residues: 1780 helix: -0.96 (0.67), residues: 45 sheet: -0.64 (0.20), residues: 633 loop : -1.40 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 249 TYR 0.019 0.002 TYR G 168 PHE 0.020 0.002 PHE G 241 TRP 0.023 0.002 TRP J 243 HIS 0.006 0.001 HIS B 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (14580) covalent geometry : angle 0.66470 / 0.34 (19784) SS BOND : bond 0.00396 / 0.22 ( 32) SS BOND : angle 1.27465 / 0.77 ( 64) hydrogen bonds : bond 0.03495 / 2.32 ( 336) hydrogen bonds : angle 6.46331 / 4.45 ( 861) link_BETA1-4 : bond 0.00121 / 0.08 ( 1) link_BETA1-4 : angle 1.01158 / 0.57 ( 3) link_NAG-ASN : bond 0.00300 / 0.13 ( 9) link_NAG-ASN : angle 1.81338 / 1.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7265 (mpp) cc_final: 0.6643 (mpp) REVERT: B 81 ASP cc_start: 0.8200 (t0) cc_final: 0.7910 (t0) REVERT: B 102 TYR cc_start: 0.7937 (m-10) cc_final: 0.7548 (m-80) REVERT: B 107 GLN cc_start: 0.8464 (tp40) cc_final: 0.7461 (tp-100) REVERT: B 137 PHE cc_start: 0.9032 (p90) cc_final: 0.8306 (p90) REVERT: B 228 GLN cc_start: 0.8026 (mt0) cc_final: 0.7697 (mt0) REVERT: A 66 LEU cc_start: 0.7383 (mm) cc_final: 0.6595 (mt) REVERT: A 88 MET cc_start: 0.9012 (ttt) cc_final: 0.8718 (ttt) REVERT: A 97 ASP cc_start: 0.8286 (p0) cc_final: 0.7631 (p0) REVERT: A 187 TYR cc_start: 0.7544 (t80) cc_final: 0.7157 (t80) REVERT: A 217 THR cc_start: 0.9002 (p) cc_final: 0.8541 (p) REVERT: A 222 LEU cc_start: 0.9396 (mt) cc_final: 0.9169 (mt) REVERT: A 235 GLN cc_start: 0.8660 (tt0) cc_final: 0.8314 (tt0) REVERT: G 76 HIS cc_start: 0.7449 (p-80) cc_final: 0.7052 (p-80) REVERT: G 77 ASP cc_start: 0.8058 (m-30) cc_final: 0.7348 (p0) REVERT: G 102 TYR cc_start: 0.8449 (m-10) cc_final: 0.7826 (m-80) REVERT: G 103 PHE cc_start: 0.8848 (m-80) cc_final: 0.8357 (m-10) REVERT: G 169 ILE cc_start: 0.9451 (mm) cc_final: 0.9169 (tp) REVERT: G 171 MET cc_start: 0.7835 (mpp) cc_final: 0.7526 (mpp) REVERT: G 262 PHE cc_start: 0.7898 (m-10) cc_final: 0.7675 (m-80) REVERT: J 59 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7815 (tm-30) REVERT: J 99 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8164 (pt0) REVERT: K 70 MET cc_start: 0.9332 (tmm) cc_final: 0.8293 (tmm) REVERT: K 89 SER cc_start: 0.8518 (p) cc_final: 0.8286 (m) REVERT: K 107 GLN cc_start: 0.9009 (tp40) cc_final: 0.8766 (mm-40) REVERT: K 235 ASP cc_start: 0.8122 (t0) cc_final: 0.7644 (t0) REVERT: K 289 HIS cc_start: 0.8957 (m-70) cc_final: 0.8567 (m90) REVERT: K 297 LEU cc_start: 0.8890 (tp) cc_final: 0.8354 (tp) REVERT: F 51 PHE cc_start: 0.8375 (p90) cc_final: 0.7482 (p90) REVERT: F 233 TYR cc_start: 0.8754 (p90) cc_final: 0.7443 (p90) REVERT: F 242 MET cc_start: 0.9363 (tpp) cc_final: 0.9108 (tpp) REVERT: H 46 GLU cc_start: 0.5101 (mp0) cc_final: 0.4526 (mp0) REVERT: H 100 PHE cc_start: 0.6486 (m-80) cc_final: 0.6236 (m-10) REVERT: L 35 TRP cc_start: 0.7504 (m100) cc_final: 0.7073 (m100) REVERT: L 69 THR cc_start: 0.8009 (m) cc_final: 0.7648 (t) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1264 time to fit residues: 57.0503 Evaluate side-chains 240 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 125 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 39 optimal weight: 0.0060 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN J 102 GLN ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.132817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.112676 restraints weight = 60098.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.114969 restraints weight = 47294.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.116095 restraints weight = 30268.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.116574 restraints weight = 23824.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.117067 restraints weight = 22689.103| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14622 Z= 0.223 Angle : 0.738 9.416 19878 Z= 0.377 Chirality : 0.048 0.279 2171 Planarity : 0.006 0.076 2525 Dihedral : 5.699 26.445 1962 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.83 (0.19), residues: 1780 helix: -1.16 (0.65), residues: 45 sheet: -0.76 (0.20), residues: 631 loop : -1.53 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 95 TYR 0.017 0.002 TYR K 15 PHE 0.030 0.002 PHE J 51 TRP 0.018 0.002 TRP K 38 HIS 0.007 0.002 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (14580) covalent geometry : angle 0.73190 / 0.38 (19784) SS BOND : bond 0.00393 / 0.21 ( 32) SS BOND : angle 1.38788 / 0.89 ( 64) hydrogen bonds : bond 0.03642 / 2.45 ( 336) hydrogen bonds : angle 6.76465 / 4.69 ( 861) link_BETA1-4 : bond 0.00828 / 0.55 ( 1) link_BETA1-4 : angle 1.12730 / 0.64 ( 3) link_NAG-ASN : bond 0.00320 / 0.15 ( 9) link_NAG-ASN : angle 1.99923 / 1.31 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7574 (mpp) cc_final: 0.6708 (mpp) REVERT: B 81 ASP cc_start: 0.8161 (t0) cc_final: 0.7911 (t0) REVERT: B 102 TYR cc_start: 0.7825 (m-10) cc_final: 0.7435 (m-80) REVERT: B 107 GLN cc_start: 0.8101 (tp40) cc_final: 0.7845 (tp40) REVERT: B 228 GLN cc_start: 0.8235 (mt0) cc_final: 0.7822 (mt0) REVERT: B 237 THR cc_start: 0.8492 (t) cc_final: 0.8140 (p) REVERT: B 333 TRP cc_start: 0.8612 (t-100) cc_final: 0.8367 (t-100) REVERT: A 46 TYR cc_start: 0.7510 (p90) cc_final: 0.6691 (p90) REVERT: A 66 LEU cc_start: 0.7304 (mm) cc_final: 0.6514 (mt) REVERT: A 97 ASP cc_start: 0.8267 (p0) cc_final: 0.8064 (p0) REVERT: A 99 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7302 (mm-30) REVERT: A 187 TYR cc_start: 0.7798 (t80) cc_final: 0.7397 (t80) REVERT: A 203 ILE cc_start: 0.8768 (mm) cc_final: 0.8562 (mm) REVERT: A 217 THR cc_start: 0.9080 (p) cc_final: 0.8628 (p) REVERT: A 222 LEU cc_start: 0.9406 (mt) cc_final: 0.9187 (mt) REVERT: A 264 GLU cc_start: 0.8880 (mp0) cc_final: 0.8570 (mp0) REVERT: G 76 HIS cc_start: 0.7442 (p-80) cc_final: 0.7078 (p-80) REVERT: G 77 ASP cc_start: 0.7917 (m-30) cc_final: 0.7248 (p0) REVERT: G 102 TYR cc_start: 0.8647 (m-10) cc_final: 0.7713 (m-80) REVERT: J 59 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7851 (tm-30) REVERT: J 99 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8191 (tt0) REVERT: J 233 TYR cc_start: 0.8437 (p90) cc_final: 0.8190 (p90) REVERT: K 15 TYR cc_start: 0.8061 (p90) cc_final: 0.7844 (p90) REVERT: K 70 MET cc_start: 0.9014 (tmm) cc_final: 0.8490 (tmm) REVERT: K 105 LEU cc_start: 0.8377 (tp) cc_final: 0.8169 (tp) REVERT: K 220 MET cc_start: 0.4741 (ttt) cc_final: 0.3293 (tpt) REVERT: K 235 ASP cc_start: 0.8350 (t0) cc_final: 0.8105 (t0) REVERT: K 333 TRP cc_start: 0.8723 (t-100) cc_final: 0.8021 (t-100) REVERT: F 51 PHE cc_start: 0.8375 (p90) cc_final: 0.7508 (p90) REVERT: F 233 TYR cc_start: 0.8926 (p90) cc_final: 0.7578 (p90) REVERT: F 242 MET cc_start: 0.9302 (tpp) cc_final: 0.9080 (tpp) REVERT: H 100 PHE cc_start: 0.6710 (m-80) cc_final: 0.6427 (m-10) REVERT: L 3 GLN cc_start: 0.5908 (tt0) cc_final: 0.5470 (tt0) REVERT: L 35 TRP cc_start: 0.7588 (m100) cc_final: 0.6695 (m100) REVERT: L 73 LEU cc_start: 0.8978 (tp) cc_final: 0.8753 (tp) outliers start: 1 outliers final: 0 residues processed: 296 average time/residue: 0.1241 time to fit residues: 53.8734 Evaluate side-chains 232 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 173 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN G 275 HIS J 204 GLN ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.135784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.115583 restraints weight = 59363.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.117695 restraints weight = 47499.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.118858 restraints weight = 31366.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.119574 restraints weight = 25418.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.119756 restraints weight = 24925.500| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.5912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14622 Z= 0.132 Angle : 0.653 8.130 19878 Z= 0.333 Chirality : 0.046 0.210 2171 Planarity : 0.005 0.068 2525 Dihedral : 5.317 25.695 1962 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.75 (0.19), residues: 1780 helix: -1.13 (0.64), residues: 45 sheet: -0.76 (0.20), residues: 630 loop : -1.43 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 50 TYR 0.018 0.002 TYR B 69 PHE 0.017 0.002 PHE L 31 TRP 0.020 0.002 TRP J 243 HIS 0.005 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14580) covalent geometry : angle 0.64843 / 0.33 (19784) SS BOND : bond 0.00299 / 0.15 ( 32) SS BOND : angle 1.23210 / 0.78 ( 64) hydrogen bonds : bond 0.03258 / 2.12 ( 336) hydrogen bonds : angle 6.38863 / 4.42 ( 861) link_BETA1-4 : bond 0.00369 / 0.25 ( 1) link_BETA1-4 : angle 0.96408 / 0.60 ( 3) link_NAG-ASN : bond 0.00260 / 0.13 ( 9) link_NAG-ASN : angle 1.55469 / 1.02 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ASP cc_start: 0.8060 (t0) cc_final: 0.7749 (t0) REVERT: B 102 TYR cc_start: 0.7866 (m-10) cc_final: 0.7435 (m-10) REVERT: B 105 LEU cc_start: 0.7548 (tt) cc_final: 0.7328 (tt) REVERT: B 107 GLN cc_start: 0.8068 (tp40) cc_final: 0.7709 (mm-40) REVERT: B 228 GLN cc_start: 0.8218 (mt0) cc_final: 0.7821 (mt0) REVERT: B 232 TYR cc_start: 0.8043 (p90) cc_final: 0.7324 (p90) REVERT: B 237 THR cc_start: 0.8485 (t) cc_final: 0.8154 (p) REVERT: A 66 LEU cc_start: 0.7278 (mm) cc_final: 0.6355 (mt) REVERT: A 97 ASP cc_start: 0.8374 (p0) cc_final: 0.7763 (p0) REVERT: A 99 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6842 (mm-30) REVERT: A 109 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 187 TYR cc_start: 0.8103 (t80) cc_final: 0.7368 (t80) REVERT: A 217 THR cc_start: 0.8892 (p) cc_final: 0.8683 (p) REVERT: A 241 GLU cc_start: 0.8515 (tp30) cc_final: 0.8209 (tp30) REVERT: A 264 GLU cc_start: 0.8826 (mp0) cc_final: 0.8500 (mp0) REVERT: G 76 HIS cc_start: 0.7348 (p-80) cc_final: 0.6976 (p-80) REVERT: G 77 ASP cc_start: 0.7720 (m-30) cc_final: 0.7261 (p0) REVERT: G 102 TYR cc_start: 0.8681 (m-10) cc_final: 0.7683 (m-80) REVERT: J 59 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7725 (tm-30) REVERT: J 99 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8087 (pt0) REVERT: J 103 LEU cc_start: 0.7476 (tp) cc_final: 0.7202 (mt) REVERT: J 233 TYR cc_start: 0.8426 (p90) cc_final: 0.7982 (p90) REVERT: K 107 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8782 (mm-40) REVERT: K 220 MET cc_start: 0.4755 (ttt) cc_final: 0.3301 (tpt) REVERT: K 235 ASP cc_start: 0.8322 (t0) cc_final: 0.8104 (t0) REVERT: K 264 LEU cc_start: 0.8786 (mt) cc_final: 0.8486 (mt) REVERT: K 333 TRP cc_start: 0.8489 (t-100) cc_final: 0.7888 (t-100) REVERT: F 51 PHE cc_start: 0.8379 (p90) cc_final: 0.7516 (p90) REVERT: F 233 TYR cc_start: 0.8914 (p90) cc_final: 0.7954 (p90) REVERT: F 242 MET cc_start: 0.9226 (tpp) cc_final: 0.9001 (tpp) REVERT: H 77 THR cc_start: 0.6000 (p) cc_final: 0.5553 (p) REVERT: H 100 PHE cc_start: 0.6625 (m-80) cc_final: 0.5780 (m-80) REVERT: L 35 TRP cc_start: 0.7290 (m100) cc_final: 0.6235 (m100) REVERT: L 69 THR cc_start: 0.7581 (p) cc_final: 0.7219 (t) REVERT: L 73 LEU cc_start: 0.8900 (tp) cc_final: 0.8673 (tp) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.1299 time to fit residues: 56.4874 Evaluate side-chains 230 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 141 optimal weight: 0.0070 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 115 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN K 125 ASN ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.136304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.115448 restraints weight = 60568.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117803 restraints weight = 41279.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.118960 restraints weight = 31339.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.119420 restraints weight = 24651.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.119525 restraints weight = 24991.940| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14622 Z= 0.120 Angle : 0.639 8.238 19878 Z= 0.324 Chirality : 0.046 0.198 2171 Planarity : 0.005 0.067 2525 Dihedral : 5.138 24.727 1962 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.06 % Allowed : 0.65 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.63 (0.19), residues: 1780 helix: -1.22 (0.63), residues: 45 sheet: -0.68 (0.20), residues: 634 loop : -1.34 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 50 TYR 0.021 0.001 TYR L 32 PHE 0.025 0.002 PHE J 51 TRP 0.024 0.002 TRP J 243 HIS 0.005 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (14580) covalent geometry : angle 0.63451 / 0.32 (19784) SS BOND : bond 0.00281 / 0.14 ( 32) SS BOND : angle 1.26167 / 0.79 ( 64) hydrogen bonds : bond 0.03208 / 2.19 ( 336) hydrogen bonds : angle 6.31722 / 4.38 ( 861) link_BETA1-4 : bond 0.00491 / 0.33 ( 1) link_BETA1-4 : angle 0.95134 / 0.57 ( 3) link_NAG-ASN : bond 0.00249 / 0.13 ( 9) link_NAG-ASN : angle 1.30942 / 0.84 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7390 (mpp) cc_final: 0.6438 (mpp) REVERT: B 102 TYR cc_start: 0.7903 (m-10) cc_final: 0.7446 (m-10) REVERT: B 179 TYR cc_start: 0.6545 (m-80) cc_final: 0.6188 (m-80) REVERT: B 228 GLN cc_start: 0.7895 (mt0) cc_final: 0.7526 (mt0) REVERT: B 237 THR cc_start: 0.8554 (t) cc_final: 0.8296 (p) REVERT: A 66 LEU cc_start: 0.7446 (mm) cc_final: 0.6714 (mt) REVERT: A 87 PHE cc_start: 0.8480 (m-10) cc_final: 0.8176 (m-10) REVERT: A 88 MET cc_start: 0.9050 (ttt) cc_final: 0.8785 (ttt) REVERT: A 97 ASP cc_start: 0.8288 (p0) cc_final: 0.8077 (p0) REVERT: A 99 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6603 (mm-30) REVERT: A 109 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 187 TYR cc_start: 0.8054 (t80) cc_final: 0.7605 (t80) REVERT: A 241 GLU cc_start: 0.8510 (tp30) cc_final: 0.8256 (tp30) REVERT: A 264 GLU cc_start: 0.8802 (mp0) cc_final: 0.8461 (mp0) REVERT: G 54 PHE cc_start: 0.8906 (m-80) cc_final: 0.8697 (m-80) REVERT: G 76 HIS cc_start: 0.7385 (p-80) cc_final: 0.6974 (p-80) REVERT: G 77 ASP cc_start: 0.7664 (m-30) cc_final: 0.7198 (p0) REVERT: G 102 TYR cc_start: 0.8675 (m-10) cc_final: 0.7673 (m-80) REVERT: G 132 LYS cc_start: 0.8760 (tmtt) cc_final: 0.8483 (tptp) REVERT: J 59 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7938 (tm-30) REVERT: J 99 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8101 (pt0) REVERT: J 103 LEU cc_start: 0.7087 (tp) cc_final: 0.6636 (mt) REVERT: J 233 TYR cc_start: 0.8501 (p90) cc_final: 0.8109 (p90) REVERT: K 89 SER cc_start: 0.8770 (p) cc_final: 0.8457 (m) REVERT: K 103 PHE cc_start: 0.8050 (m-10) cc_final: 0.7841 (m-10) REVERT: K 220 MET cc_start: 0.4902 (ttt) cc_final: 0.3468 (tpt) REVERT: K 264 LEU cc_start: 0.8735 (mt) cc_final: 0.8476 (mt) REVERT: K 333 TRP cc_start: 0.8456 (t-100) cc_final: 0.7986 (t-100) REVERT: F 51 PHE cc_start: 0.8376 (p90) cc_final: 0.7588 (p90) REVERT: F 233 TYR cc_start: 0.9012 (p90) cc_final: 0.7925 (p90) REVERT: F 242 MET cc_start: 0.9256 (tpp) cc_final: 0.9029 (tpp) REVERT: H 46 GLU cc_start: 0.6456 (mp0) cc_final: 0.6121 (mp0) REVERT: L 3 GLN cc_start: 0.5845 (tt0) cc_final: 0.5365 (tt0) REVERT: L 24 ARG cc_start: 0.4504 (ptt180) cc_final: 0.3791 (ptt-90) REVERT: L 35 TRP cc_start: 0.7253 (m100) cc_final: 0.6739 (m100) REVERT: L 73 LEU cc_start: 0.8914 (tp) cc_final: 0.8624 (tp) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.1205 time to fit residues: 52.1877 Evaluate side-chains 236 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 4 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN J 118 HIS ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.133476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.111956 restraints weight = 60676.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.113949 restraints weight = 43750.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115374 restraints weight = 31691.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.115870 restraints weight = 25489.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.116078 restraints weight = 24417.065| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14622 Z= 0.187 Angle : 0.705 8.820 19878 Z= 0.357 Chirality : 0.047 0.254 2171 Planarity : 0.006 0.065 2525 Dihedral : 5.383 24.880 1962 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.06 % Allowed : 0.32 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.81 (0.19), residues: 1780 helix: -1.18 (0.64), residues: 45 sheet: -0.88 (0.20), residues: 640 loop : -1.42 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 50 TYR 0.021 0.002 TYR L 32 PHE 0.021 0.002 PHE J 170 TRP 0.025 0.002 TRP J 243 HIS 0.011 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (14580) covalent geometry : angle 0.69934 / 0.36 (19784) SS BOND : bond 0.00305 / 0.19 ( 32) SS BOND : angle 1.37216 / 0.89 ( 64) hydrogen bonds : bond 0.03450 / 2.32 ( 336) hydrogen bonds : angle 6.61010 / 4.58 ( 861) link_BETA1-4 : bond 0.00576 / 0.38 ( 1) link_BETA1-4 : angle 1.04056 / 0.61 ( 3) link_NAG-ASN : bond 0.00242 / 0.12 ( 9) link_NAG-ASN : angle 1.61517 / 1.06 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 LEU cc_start: 0.8466 (pt) cc_final: 0.8156 (pt) REVERT: B 70 MET cc_start: 0.7438 (mpp) cc_final: 0.6378 (mpp) REVERT: B 102 TYR cc_start: 0.7745 (m-10) cc_final: 0.7315 (m-10) REVERT: B 107 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7765 (mm-40) REVERT: B 179 TYR cc_start: 0.6910 (m-80) cc_final: 0.6516 (m-80) REVERT: B 228 GLN cc_start: 0.7944 (mt0) cc_final: 0.7613 (mt0) REVERT: B 237 THR cc_start: 0.8533 (t) cc_final: 0.8208 (p) REVERT: A 66 LEU cc_start: 0.7266 (mm) cc_final: 0.6462 (mt) REVERT: A 97 ASP cc_start: 0.8288 (p0) cc_final: 0.7558 (p0) REVERT: A 99 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6860 (mm-30) REVERT: A 241 GLU cc_start: 0.8452 (tp30) cc_final: 0.8240 (tp30) REVERT: A 264 GLU cc_start: 0.8852 (mp0) cc_final: 0.8521 (mp0) REVERT: G 54 PHE cc_start: 0.8975 (m-80) cc_final: 0.8720 (m-80) REVERT: G 76 HIS cc_start: 0.7818 (p-80) cc_final: 0.7587 (p-80) REVERT: G 77 ASP cc_start: 0.8154 (m-30) cc_final: 0.7544 (p0) REVERT: G 79 LYS cc_start: 0.7722 (pttm) cc_final: 0.7317 (mptt) REVERT: G 102 TYR cc_start: 0.8647 (m-10) cc_final: 0.7692 (m-80) REVERT: G 103 PHE cc_start: 0.8273 (m-80) cc_final: 0.7983 (m-10) REVERT: G 132 LYS cc_start: 0.8808 (tmtt) cc_final: 0.8488 (tptp) REVERT: J 59 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7982 (tm-30) REVERT: J 99 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8143 (pt0) REVERT: J 103 LEU cc_start: 0.7199 (tp) cc_final: 0.6881 (mt) REVERT: J 233 TYR cc_start: 0.8533 (p90) cc_final: 0.8246 (p90) REVERT: J 242 MET cc_start: 0.8605 (tpt) cc_final: 0.8349 (tpt) REVERT: K 105 LEU cc_start: 0.8521 (tp) cc_final: 0.8290 (tt) REVERT: K 220 MET cc_start: 0.5190 (ttt) cc_final: 0.3834 (tpt) REVERT: K 264 LEU cc_start: 0.8784 (mt) cc_final: 0.8557 (mt) REVERT: K 313 TRP cc_start: 0.9260 (m100) cc_final: 0.8605 (m100) REVERT: K 333 TRP cc_start: 0.8546 (t-100) cc_final: 0.7934 (t-100) REVERT: F 51 PHE cc_start: 0.8288 (p90) cc_final: 0.7395 (p90) REVERT: F 233 TYR cc_start: 0.9122 (p90) cc_final: 0.8004 (p90) REVERT: F 235 GLN cc_start: 0.7998 (mm110) cc_final: 0.7794 (mm110) REVERT: F 242 MET cc_start: 0.9234 (tpp) cc_final: 0.9020 (tpp) REVERT: L 35 TRP cc_start: 0.7448 (m100) cc_final: 0.7157 (m100) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.1157 time to fit residues: 48.5914 Evaluate side-chains 222 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 113 optimal weight: 0.0980 chunk 87 optimal weight: 0.0050 chunk 4 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 123 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN K 125 ASN ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.116339 restraints weight = 60063.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.118541 restraints weight = 42694.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.119596 restraints weight = 32938.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.119854 restraints weight = 26008.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.120437 restraints weight = 25577.573| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14622 Z= 0.117 Angle : 0.650 8.117 19878 Z= 0.329 Chirality : 0.047 0.200 2171 Planarity : 0.005 0.061 2525 Dihedral : 5.104 24.035 1962 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.06 % Allowed : 0.32 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % 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: -1.65 (0.19), residues: 1780 helix: -1.42 (0.63), residues: 45 sheet: -0.74 (0.20), residues: 626 loop : -1.31 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 50 TYR 0.022 0.001 TYR L 32 PHE 0.026 0.002 PHE J 51 TRP 0.022 0.002 TRP L 35 HIS 0.009 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14580) covalent geometry : angle 0.64599 / 0.33 (19784) SS BOND : bond 0.00298 / 0.15 ( 32) SS BOND : angle 1.24284 / 0.80 ( 64) hydrogen bonds : bond 0.03155 / 2.11 ( 336) hydrogen bonds : angle 6.21883 / 4.30 ( 861) link_BETA1-4 : bond 0.00675 / 0.45 ( 1) link_BETA1-4 : angle 1.02163 / 0.63 ( 3) link_NAG-ASN : bond 0.00269 / 0.15 ( 9) link_NAG-ASN : angle 1.26433 / 0.81 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3100.85 seconds wall clock time: 54 minutes 35.52 seconds (3275.52 seconds total)