Starting phenix.real_space_refine on Sat Oct 11 11:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dul_27722/10_2025/8dul_27722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dul_27722/10_2025/8dul_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dul_27722/10_2025/8dul_27722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dul_27722/10_2025/8dul_27722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dul_27722/10_2025/8dul_27722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dul_27722/10_2025/8dul_27722.map" } 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-2.0-5842/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.58, per 1000 atoms: 0.25 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: 1.14 Conformation dependent library (CDL) restraints added in 659.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.66 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: 2.36 Time building geometry restraints manager: 1.54 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: 8089 17.67 - 35.34: 658 35.34 - 53.00: 123 53.00 - 70.67: 14 70.67 - 88.34: 12 Dihedral angle restraints: 8896 sinusoidal: 3686 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 8893 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: 23.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.220 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5086 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 : 13.085 88.339 5464 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 aren 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 covalent geometry : bond 0.00498 (14580) covalent geometry : angle 1.04376 (19784) SS BOND : bond 0.00430 ( 32) SS BOND : angle 1.43959 ( 64) hydrogen bonds : bond 0.28484 ( 336) hydrogen bonds : angle 10.36012 ( 861) link_BETA1-4 : bond 0.00660 ( 1) link_BETA1-4 : angle 1.50224 ( 3) link_NAG-ASN : bond 0.00526 ( 9) link_NAG-ASN : angle 4.73238 ( 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 : 0.563 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: 0.7475 (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: 0.1427 time to fit residues: 92.3488 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 : 0.568 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4262 r_free = 0.4262 target = 0.142841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.122550 restraints weight = 60150.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.125884 restraints weight = 38670.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.127020 restraints weight = 26878.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.127928 restraints weight = 21561.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.128325 restraints weight = 17944.632| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14622 Z= 0.177 Angle : 0.685 7.911 19878 Z= 0.355 Chirality : 0.046 0.237 2171 Planarity : 0.006 0.066 2525 Dihedral : 5.995 48.322 2172 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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 aren not related in a simple way. whole: -1.63 (0.18), residues: 1780 helix: -1.51 (0.70), residues: 45 sheet: -0.49 (0.22), residues: 519 loop : -1.40 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 79 TYR 0.013 0.002 TYR F 187 PHE 0.017 0.002 PHE A 95 TRP 0.026 0.002 TRP F 243 HIS 0.009 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00381 (14580) covalent geometry : angle 0.67740 (19784) SS BOND : bond 0.00312 ( 32) SS BOND : angle 1.04975 ( 64) hydrogen bonds : bond 0.04253 ( 336) hydrogen bonds : angle 6.99835 ( 861) link_BETA1-4 : bond 0.00350 ( 1) link_BETA1-4 : angle 1.23343 ( 3) link_NAG-ASN : bond 0.00588 ( 9) link_NAG-ASN : angle 2.57080 ( 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 : 0.565 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: 0.7068 (mpp) cc_final: 0.6405 (mpp) REVERT: B 81 ASP cc_start: 0.7747 (t0) cc_final: 0.7399 (t0) REVERT: B 102 TYR cc_start: 0.7466 (m-80) cc_final: 0.7246 (m-10) REVERT: B 105 LEU cc_start: 0.7402 (tt) cc_final: 0.7100 (tp) REVERT: B 107 GLN cc_start: 0.8263 (mm-40) cc_final: 0.7850 (mm-40) REVERT: B 240 VAL cc_start: 0.9562 (m) cc_final: 0.9358 (p) REVERT: A 97 ASP cc_start: 0.8323 (p0) cc_final: 0.7685 (p0) REVERT: A 118 HIS cc_start: 0.9358 (p-80) cc_final: 0.8970 (p-80) REVERT: A 217 THR cc_start: 0.8694 (p) cc_final: 0.8439 (p) REVERT: A 219 ILE cc_start: 0.8964 (tp) cc_final: 0.8467 (tp) REVERT: A 220 ARG cc_start: 0.8140 (mpp80) cc_final: 0.7579 (ptt-90) REVERT: G 38 TRP cc_start: 0.8824 (m-90) cc_final: 0.8409 (m-90) REVERT: G 64 VAL cc_start: 0.8570 (p) cc_final: 0.8246 (p) REVERT: G 81 ASP cc_start: 0.7567 (m-30) cc_final: 0.7238 (m-30) REVERT: G 235 ASP cc_start: 0.7675 (m-30) cc_final: 0.7461 (m-30) REVERT: J 99 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7971 (pt0) REVERT: J 233 TYR cc_start: 0.8571 (p90) cc_final: 0.8235 (p90) REVERT: K 38 TRP cc_start: 0.8647 (m-90) cc_final: 0.8320 (m-90) REVERT: K 235 ASP cc_start: 0.7980 (t0) cc_final: 0.7581 (t0) REVERT: K 241 PHE cc_start: 0.8484 (t80) cc_final: 0.8125 (t80) REVERT: K 262 PHE cc_start: 0.7231 (m-80) cc_final: 0.5958 (m-10) REVERT: K 289 HIS cc_start: 0.8692 (m-70) cc_final: 0.8370 (m-70) REVERT: K 336 HIS cc_start: 0.6362 (m90) cc_final: 0.5822 (m-70) REVERT: F 51 PHE cc_start: 0.8180 (p90) cc_final: 0.7387 (p90) REVERT: F 103 LEU cc_start: 0.8252 (tp) cc_final: 0.7895 (tt) REVERT: F 117 ASP cc_start: 0.8196 (p0) cc_final: 0.7981 (t0) REVERT: F 233 TYR cc_start: 0.8686 (p90) cc_final: 0.7715 (p90) REVERT: F 242 MET cc_start: 0.9472 (tpp) cc_final: 0.9218 (tpp) REVERT: H 66 ARG cc_start: -0.2077 (mmt180) cc_final: -0.3167 (mmm160) REVERT: H 96 ASP cc_start: 0.8411 (p0) cc_final: 0.8109 (p0) REVERT: L 3 GLN cc_start: 0.3876 (tt0) cc_final: 0.3531 (tt0) REVERT: L 5 THR cc_start: 0.8048 (p) cc_final: 0.7838 (p) REVERT: L 45 LYS cc_start: 0.8603 (tptp) cc_final: 0.8291 (tppt) REVERT: L 69 THR cc_start: 0.7728 (m) cc_final: 0.7415 (t) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1265 time to fit residues: 63.5716 Evaluate side-chains 242 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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: 8.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 0.0030 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 A 230 HIS J 230 HIS K 259 HIS F 102 GLN ** F 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.140251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.120384 restraints weight = 59978.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.122310 restraints weight = 42424.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.124278 restraints weight = 29969.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.124407 restraints weight = 23846.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.125036 restraints weight = 21164.909| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 14622 Z= 0.171 Angle : 0.650 13.537 19878 Z= 0.338 Chirality : 0.045 0.211 2171 Planarity : 0.005 0.069 2525 Dihedral : 5.778 51.026 2172 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % 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 aren not related in a simple way. whole: -1.49 (0.19), residues: 1780 helix: -1.21 (0.72), residues: 45 sheet: -0.37 (0.20), residues: 600 loop : -1.37 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 50 TYR 0.016 0.002 TYR A 46 PHE 0.023 0.002 PHE A 189 TRP 0.016 0.002 TRP F 243 HIS 0.008 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00387 (14580) covalent geometry : angle 0.63668 (19784) SS BOND : bond 0.00575 ( 32) SS BOND : angle 2.11850 ( 64) hydrogen bonds : bond 0.03894 ( 336) hydrogen bonds : angle 6.57217 ( 861) link_BETA1-4 : bond 0.00450 ( 1) link_BETA1-4 : angle 0.86658 ( 3) link_NAG-ASN : bond 0.00326 ( 9) link_NAG-ASN : angle 1.86982 ( 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 324 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 0.556 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: B 36 ASN cc_start: 0.8401 (t0) cc_final: 0.7881 (t0) REVERT: B 81 ASP cc_start: 0.7756 (t0) cc_final: 0.7382 (t0) REVERT: B 102 TYR cc_start: 0.7997 (m-80) cc_final: 0.7708 (m-80) REVERT: B 105 LEU cc_start: 0.7382 (tt) cc_final: 0.7140 (tp) REVERT: B 107 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7575 (mm-40) REVERT: B 137 PHE cc_start: 0.9031 (p90) cc_final: 0.8141 (p90) REVERT: B 333 TRP cc_start: 0.8224 (t-100) cc_final: 0.7887 (t-100) REVERT: A 87 PHE cc_start: 0.8712 (m-10) cc_final: 0.8378 (m-10) REVERT: A 97 ASP cc_start: 0.8342 (p0) cc_final: 0.7728 (p0) REVERT: A 99 GLU cc_start: 0.7176 (tp30) cc_final: 0.6856 (tp30) REVERT: A 187 TYR cc_start: 0.7192 (t80) cc_final: 0.6789 (t80) REVERT: A 202 ASP cc_start: 0.8062 (p0) cc_final: 0.7186 (t0) REVERT: A 219 ILE cc_start: 0.9074 (tp) cc_final: 0.8625 (tp) REVERT: A 220 ARG cc_start: 0.8018 (mpp80) cc_final: 0.7623 (ptt-90) REVERT: G 38 TRP cc_start: 0.9062 (m-90) cc_final: 0.8371 (m-90) REVERT: G 95 ARG cc_start: 0.8582 (tmm-80) cc_final: 0.8320 (tmm-80) REVERT: G 329 LEU cc_start: 0.7640 (tt) cc_final: 0.7425 (tt) REVERT: J 99 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7865 (pt0) REVERT: J 233 TYR cc_start: 0.8584 (p90) cc_final: 0.8364 (p90) REVERT: K 23 ARG cc_start: 0.8567 (ptt90) cc_final: 0.7837 (tmm-80) REVERT: K 180 LYS cc_start: 0.8623 (ptpp) cc_final: 0.8243 (mtmm) REVERT: K 235 ASP cc_start: 0.7848 (t0) cc_final: 0.7309 (t0) REVERT: K 289 HIS cc_start: 0.8864 (m-70) cc_final: 0.8510 (m-70) REVERT: K 336 HIS cc_start: 0.6193 (m90) cc_final: 0.5769 (m-70) REVERT: F 51 PHE cc_start: 0.8302 (p90) cc_final: 0.7426 (p90) REVERT: F 103 LEU cc_start: 0.8329 (tp) cc_final: 0.7817 (tt) REVERT: F 233 TYR cc_start: 0.8506 (p90) cc_final: 0.7333 (p90) REVERT: F 242 MET cc_start: 0.9401 (tpp) cc_final: 0.9171 (tpp) REVERT: H 66 ARG cc_start: 0.0113 (mmt180) cc_final: -0.0137 (mmm160) REVERT: H 100 PHE cc_start: 0.7462 (m-80) cc_final: 0.7113 (m-80) REVERT: L 36 TYR cc_start: 0.5868 (m-80) cc_final: 0.5601 (m-80) REVERT: L 69 THR cc_start: 0.7667 (m) cc_final: 0.7251 (t) outliers start: 1 outliers final: 0 residues processed: 323 average time/residue: 0.1335 time to fit residues: 61.9598 Evaluate side-chains 245 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 0.0770 chunk 170 optimal weight: 0.0040 chunk 83 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN A 59 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 HIS F 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.141290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.121328 restraints weight = 60499.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123517 restraints weight = 42006.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.124560 restraints weight = 32656.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.125110 restraints weight = 25466.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.125431 restraints weight = 24500.181| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14622 Z= 0.113 Angle : 0.596 6.970 19878 Z= 0.308 Chirality : 0.045 0.216 2171 Planarity : 0.005 0.072 2525 Dihedral : 5.408 51.592 2172 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.06 % Allowed : 3.50 % 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 aren not related in a simple way. whole: -1.50 (0.19), residues: 1780 helix: -1.19 (0.72), residues: 45 sheet: -0.40 (0.20), residues: 609 loop : -1.37 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 50 TYR 0.017 0.001 TYR G 168 PHE 0.020 0.001 PHE A 95 TRP 0.010 0.001 TRP F 243 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00261 (14580) covalent geometry : angle 0.59189 (19784) SS BOND : bond 0.00294 ( 32) SS BOND : angle 0.95446 ( 64) hydrogen bonds : bond 0.03411 ( 336) hydrogen bonds : angle 6.12605 ( 861) link_BETA1-4 : bond 0.00213 ( 1) link_BETA1-4 : angle 0.93024 ( 3) link_NAG-ASN : bond 0.00281 ( 9) link_NAG-ASN : angle 1.49007 ( 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 332 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 0.541 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 36 ASN cc_start: 0.8235 (t0) cc_final: 0.7707 (t0) REVERT: B 81 ASP cc_start: 0.7709 (t0) cc_final: 0.7319 (t0) REVERT: B 105 LEU cc_start: 0.7261 (tt) cc_final: 0.6978 (tp) REVERT: B 107 GLN cc_start: 0.7731 (mm-40) cc_final: 0.6877 (tp-100) REVERT: B 137 PHE cc_start: 0.9049 (p90) cc_final: 0.8154 (p90) REVERT: B 228 GLN cc_start: 0.7986 (mt0) cc_final: 0.7615 (mt0) REVERT: B 333 TRP cc_start: 0.8307 (t-100) cc_final: 0.7967 (t-100) REVERT: A 97 ASP cc_start: 0.8296 (p0) cc_final: 0.7671 (p0) REVERT: A 99 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6767 (tp30) REVERT: A 187 TYR cc_start: 0.7487 (t80) cc_final: 0.7029 (t80) REVERT: A 217 THR cc_start: 0.8444 (p) cc_final: 0.8134 (p) REVERT: G 36 ASN cc_start: 0.9083 (t0) cc_final: 0.8856 (t0) REVERT: G 38 TRP cc_start: 0.9126 (m-90) cc_final: 0.8806 (m-90) REVERT: G 49 GLN cc_start: 0.6905 (tm-30) cc_final: 0.6278 (tm-30) REVERT: G 95 ARG cc_start: 0.8613 (tmm-80) cc_final: 0.8324 (tmm-80) REVERT: J 59 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7910 (tm-30) REVERT: J 99 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8072 (pt0) REVERT: K 15 TYR cc_start: 0.8230 (p90) cc_final: 0.7411 (p90) REVERT: K 220 MET cc_start: 0.4670 (ttt) cc_final: 0.3356 (tpt) REVERT: K 235 ASP cc_start: 0.7795 (t0) cc_final: 0.7180 (t0) REVERT: K 241 PHE cc_start: 0.8585 (t80) cc_final: 0.8221 (t80) REVERT: K 262 PHE cc_start: 0.7288 (m-80) cc_final: 0.6364 (m-10) REVERT: K 289 HIS cc_start: 0.8793 (m-70) cc_final: 0.8495 (m-70) REVERT: K 336 HIS cc_start: 0.6774 (m90) cc_final: 0.6058 (m-70) REVERT: F 51 PHE cc_start: 0.8338 (p90) cc_final: 0.7457 (p90) REVERT: F 233 TYR cc_start: 0.8491 (p90) cc_final: 0.7348 (p90) REVERT: F 242 MET cc_start: 0.9426 (tpp) cc_final: 0.9210 (tpp) REVERT: H 66 ARG cc_start: 0.0390 (mmt180) cc_final: -0.0419 (mmm160) REVERT: H 77 THR cc_start: 0.6067 (p) cc_final: 0.5827 (p) REVERT: H 100 PHE cc_start: 0.7485 (m-80) cc_final: 0.6922 (m-80) REVERT: L 3 GLN cc_start: 0.1141 (tt0) cc_final: 0.0885 (tt0) REVERT: L 69 THR cc_start: 0.7861 (m) cc_final: 0.7471 (t) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.1328 time to fit residues: 63.5232 Evaluate side-chains 244 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 3.9990 chunk 161 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 46 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 123 optimal weight: 0.0970 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 125 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4235 r_free = 0.4235 target = 0.141294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.122450 restraints weight = 61005.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.124704 restraints weight = 42762.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.125718 restraints weight = 32431.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.126479 restraints weight = 25180.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.127025 restraints weight = 22872.023| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14622 Z= 0.115 Angle : 0.596 7.051 19878 Z= 0.306 Chirality : 0.045 0.210 2171 Planarity : 0.005 0.067 2525 Dihedral : 5.334 51.710 2172 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.61 % 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 aren not related in a simple way. whole: -1.40 (0.19), residues: 1780 helix: -1.16 (0.72), residues: 45 sheet: -0.28 (0.20), residues: 620 loop : -1.34 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 50 TYR 0.019 0.001 TYR A 85 PHE 0.015 0.001 PHE A 95 TRP 0.023 0.001 TRP K 282 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00263 (14580) covalent geometry : angle 0.58824 (19784) SS BOND : bond 0.00311 ( 32) SS BOND : angle 1.35735 ( 64) hydrogen bonds : bond 0.03234 ( 336) hydrogen bonds : angle 5.96148 ( 861) link_BETA1-4 : bond 0.00663 ( 1) link_BETA1-4 : angle 1.13217 ( 3) link_NAG-ASN : bond 0.00596 ( 9) link_NAG-ASN : angle 1.81992 ( 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 315 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.566 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 105 LEU cc_start: 0.7655 (tt) cc_final: 0.7325 (tp) REVERT: B 137 PHE cc_start: 0.8974 (p90) cc_final: 0.8092 (p90) REVERT: B 228 GLN cc_start: 0.7998 (mt0) cc_final: 0.7660 (mt0) REVERT: B 333 TRP cc_start: 0.8249 (t-100) cc_final: 0.7953 (t-100) REVERT: A 97 ASP cc_start: 0.8299 (p0) cc_final: 0.7656 (p0) REVERT: A 99 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6786 (mm-30) REVERT: A 187 TYR cc_start: 0.7482 (t80) cc_final: 0.7066 (t80) REVERT: A 202 ASP cc_start: 0.7765 (p0) cc_final: 0.7242 (t0) REVERT: G 36 ASN cc_start: 0.9062 (t0) cc_final: 0.8838 (t0) REVERT: G 38 TRP cc_start: 0.9152 (m-90) cc_final: 0.8834 (m-90) REVERT: G 49 GLN cc_start: 0.6869 (tm-30) cc_final: 0.6249 (tm-30) REVERT: G 76 HIS cc_start: 0.7440 (p-80) cc_final: 0.7224 (p-80) REVERT: G 77 ASP cc_start: 0.8334 (m-30) cc_final: 0.7492 (p0) REVERT: G 95 ARG cc_start: 0.8565 (tmm-80) cc_final: 0.8271 (tmm-80) REVERT: G 103 PHE cc_start: 0.7957 (m-10) cc_final: 0.7290 (m-10) REVERT: G 235 ASP cc_start: 0.9147 (t0) cc_final: 0.8878 (t0) REVERT: J 59 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7961 (tm-30) REVERT: J 99 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8000 (pt0) REVERT: J 219 ILE cc_start: 0.8587 (tp) cc_final: 0.8233 (mm) REVERT: J 233 TYR cc_start: 0.8451 (p90) cc_final: 0.8080 (p90) REVERT: K 15 TYR cc_start: 0.8203 (p90) cc_final: 0.7461 (p90) REVERT: K 220 MET cc_start: 0.4511 (ttt) cc_final: 0.3177 (tpt) REVERT: K 235 ASP cc_start: 0.7831 (t0) cc_final: 0.7243 (t0) REVERT: K 241 PHE cc_start: 0.8610 (t80) cc_final: 0.8240 (t80) REVERT: K 262 PHE cc_start: 0.7407 (m-80) cc_final: 0.6508 (m-10) REVERT: K 289 HIS cc_start: 0.8538 (m-70) cc_final: 0.8286 (m-70) REVERT: F 51 PHE cc_start: 0.8116 (p90) cc_final: 0.7189 (p90) REVERT: F 233 TYR cc_start: 0.8458 (p90) cc_final: 0.7385 (p90) REVERT: F 242 MET cc_start: 0.9368 (tpp) cc_final: 0.9135 (tpp) REVERT: H 66 ARG cc_start: 0.0775 (mmt180) cc_final: -0.0029 (mmm160) REVERT: H 100 PHE cc_start: 0.7198 (m-80) cc_final: 0.6940 (m-10) REVERT: L 45 LYS cc_start: 0.8614 (tptp) cc_final: 0.8313 (tppt) REVERT: L 69 THR cc_start: 0.7945 (m) cc_final: 0.7659 (t) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.1354 time to fit residues: 60.9700 Evaluate side-chains 242 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 2.9990 chunk 117 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.0050 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 255 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN K 156 HIS F 100 ASN H 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.116062 restraints weight = 61449.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.117415 restraints weight = 44524.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.117978 restraints weight = 36985.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.118735 restraints weight = 30993.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.119437 restraints weight = 26779.162| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14622 Z= 0.215 Angle : 0.709 9.902 19878 Z= 0.361 Chirality : 0.046 0.250 2171 Planarity : 0.006 0.074 2525 Dihedral : 5.817 53.894 2172 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % 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 aren not related in a simple way. whole: -1.63 (0.19), residues: 1780 helix: -1.16 (0.66), residues: 45 sheet: -0.57 (0.20), residues: 629 loop : -1.43 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 306 TYR 0.017 0.002 TYR G 168 PHE 0.023 0.002 PHE J 170 TRP 0.033 0.003 TRP H 103 HIS 0.010 0.002 HIS K 336 Details of bonding type rmsd covalent geometry : bond 0.00466 (14580) covalent geometry : angle 0.70199 (19784) SS BOND : bond 0.00410 ( 32) SS BOND : angle 1.32998 ( 64) hydrogen bonds : bond 0.03814 ( 336) hydrogen bonds : angle 6.39793 ( 861) link_BETA1-4 : bond 0.00152 ( 1) link_BETA1-4 : angle 1.23933 ( 3) link_NAG-ASN : bond 0.00281 ( 9) link_NAG-ASN : angle 2.05824 ( 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 307 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 0.591 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: B 70 MET cc_start: 0.7259 (mpp) cc_final: 0.6150 (mpp) REVERT: B 81 ASP cc_start: 0.7813 (t0) cc_final: 0.7427 (t0) REVERT: B 107 GLN cc_start: 0.8443 (tp-100) cc_final: 0.7784 (mm-40) REVERT: B 137 PHE cc_start: 0.9058 (p90) cc_final: 0.8371 (p90) REVERT: B 228 GLN cc_start: 0.7936 (mt0) cc_final: 0.7490 (mt0) REVERT: A 66 LEU cc_start: 0.7428 (mm) cc_final: 0.6747 (mt) REVERT: A 97 ASP cc_start: 0.8310 (p0) cc_final: 0.7641 (p0) REVERT: A 99 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7055 (mm-30) REVERT: A 187 TYR cc_start: 0.7868 (t80) cc_final: 0.7350 (t80) REVERT: A 202 ASP cc_start: 0.8163 (p0) cc_final: 0.7802 (t0) REVERT: G 36 ASN cc_start: 0.9242 (t0) cc_final: 0.9000 (t0) REVERT: G 49 GLN cc_start: 0.6077 (tm-30) cc_final: 0.5319 (tm-30) REVERT: G 76 HIS cc_start: 0.7589 (p-80) cc_final: 0.7185 (p-80) REVERT: G 77 ASP cc_start: 0.7857 (m-30) cc_final: 0.7236 (p0) REVERT: G 79 LYS cc_start: 0.7549 (mppt) cc_final: 0.7324 (pttm) REVERT: G 95 ARG cc_start: 0.8691 (tmm-80) cc_final: 0.8430 (tmm-80) REVERT: G 102 TYR cc_start: 0.8614 (m-10) cc_final: 0.8373 (m-10) REVERT: J 59 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7911 (tm-30) REVERT: J 88 MET cc_start: 0.7326 (tpt) cc_final: 0.7124 (tpp) REVERT: J 99 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8093 (pt0) REVERT: J 184 VAL cc_start: 0.7040 (m) cc_final: 0.6827 (m) REVERT: K 15 TYR cc_start: 0.8276 (p90) cc_final: 0.7747 (p90) REVERT: K 68 ARG cc_start: 0.6732 (ptp-170) cc_final: 0.6284 (ptp-110) REVERT: K 220 MET cc_start: 0.4941 (ttt) cc_final: 0.3544 (tpt) REVERT: K 235 ASP cc_start: 0.8070 (t0) cc_final: 0.7568 (t0) REVERT: K 241 PHE cc_start: 0.8820 (t80) cc_final: 0.8482 (t80) REVERT: K 262 PHE cc_start: 0.7599 (m-80) cc_final: 0.6143 (m-10) REVERT: K 289 HIS cc_start: 0.8971 (m-70) cc_final: 0.8644 (m90) REVERT: F 51 PHE cc_start: 0.8317 (p90) cc_final: 0.7449 (p90) REVERT: F 113 ASP cc_start: 0.6948 (p0) cc_final: 0.6682 (p0) REVERT: F 233 TYR cc_start: 0.8543 (p90) cc_final: 0.7202 (p90) REVERT: F 242 MET cc_start: 0.9381 (tpp) cc_final: 0.9142 (tpp) REVERT: H 46 GLU cc_start: 0.5266 (mp0) cc_final: 0.4696 (mp0) REVERT: H 100 PHE cc_start: 0.6799 (m-80) cc_final: 0.6476 (m-10) REVERT: L 35 TRP cc_start: 0.7551 (m100) cc_final: 0.7226 (m100) REVERT: L 69 THR cc_start: 0.7879 (m) cc_final: 0.7532 (t) REVERT: L 73 LEU cc_start: 0.9032 (tp) cc_final: 0.8698 (tp) outliers start: 1 outliers final: 0 residues processed: 307 average time/residue: 0.1345 time to fit residues: 59.1071 Evaluate side-chains 219 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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: 1.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 GLN B 156 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.135840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.116751 restraints weight = 60538.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.118386 restraints weight = 45217.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.119049 restraints weight = 34225.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.119802 restraints weight = 26781.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.120254 restraints weight = 24230.897| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14622 Z= 0.179 Angle : 0.663 7.814 19878 Z= 0.340 Chirality : 0.047 0.255 2171 Planarity : 0.005 0.068 2525 Dihedral : 5.736 52.762 2172 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 aren not related in a simple way. whole: -1.66 (0.18), residues: 1780 helix: -1.18 (0.64), residues: 45 sheet: -0.52 (0.21), residues: 561 loop : -1.45 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 263 TYR 0.020 0.002 TYR L 32 PHE 0.016 0.002 PHE K 283 TRP 0.021 0.002 TRP H 103 HIS 0.006 0.001 HIS H 101 Details of bonding type rmsd covalent geometry : bond 0.00398 (14580) covalent geometry : angle 0.65738 (19784) SS BOND : bond 0.00643 ( 32) SS BOND : angle 1.29636 ( 64) hydrogen bonds : bond 0.03429 ( 336) hydrogen bonds : angle 6.38010 ( 861) link_BETA1-4 : bond 0.00531 ( 1) link_BETA1-4 : angle 1.04237 ( 3) link_NAG-ASN : bond 0.00247 ( 9) link_NAG-ASN : angle 1.81544 ( 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 303 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.568 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: B 70 MET cc_start: 0.6977 (mpp) cc_final: 0.5965 (mpp) REVERT: B 81 ASP cc_start: 0.8026 (t0) cc_final: 0.7738 (t0) REVERT: B 107 GLN cc_start: 0.8549 (tp40) cc_final: 0.7982 (mm-40) REVERT: B 179 TYR cc_start: 0.6640 (m-80) cc_final: 0.6227 (m-80) REVERT: B 228 GLN cc_start: 0.8026 (mt0) cc_final: 0.7603 (mt0) REVERT: B 232 TYR cc_start: 0.8115 (p90) cc_final: 0.7395 (p90) REVERT: B 237 THR cc_start: 0.8554 (t) cc_final: 0.8287 (p) REVERT: A 66 LEU cc_start: 0.7461 (mm) cc_final: 0.6673 (mt) REVERT: A 97 ASP cc_start: 0.8405 (p0) cc_final: 0.7779 (p0) REVERT: A 99 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7107 (mm-30) REVERT: A 109 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 187 TYR cc_start: 0.7975 (t80) cc_final: 0.7578 (t80) REVERT: A 202 ASP cc_start: 0.8150 (p0) cc_final: 0.7613 (t0) REVERT: A 217 THR cc_start: 0.8106 (p) cc_final: 0.7857 (p) REVERT: A 219 ILE cc_start: 0.8776 (tp) cc_final: 0.8267 (tp) REVERT: A 235 GLN cc_start: 0.8721 (tt0) cc_final: 0.7865 (tt0) REVERT: A 264 GLU cc_start: 0.8660 (mp0) cc_final: 0.8451 (mp0) REVERT: G 36 ASN cc_start: 0.9194 (t0) cc_final: 0.8766 (t0) REVERT: G 76 HIS cc_start: 0.7494 (p-80) cc_final: 0.7064 (p-80) REVERT: G 77 ASP cc_start: 0.7796 (m-30) cc_final: 0.7346 (p0) REVERT: G 79 LYS cc_start: 0.7622 (mppt) cc_final: 0.7383 (pttm) REVERT: G 103 PHE cc_start: 0.8384 (m-10) cc_final: 0.7776 (m-10) REVERT: J 59 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7873 (tm-30) REVERT: J 88 MET cc_start: 0.7162 (tpt) cc_final: 0.6919 (tpp) REVERT: J 99 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8071 (pt0) REVERT: J 233 TYR cc_start: 0.8421 (p90) cc_final: 0.8015 (p90) REVERT: K 220 MET cc_start: 0.4838 (ttt) cc_final: 0.3553 (tpt) REVERT: K 235 ASP cc_start: 0.7980 (t0) cc_final: 0.7542 (t0) REVERT: K 289 HIS cc_start: 0.8924 (m-70) cc_final: 0.8550 (m90) REVERT: F 51 PHE cc_start: 0.8374 (p90) cc_final: 0.7558 (p90) REVERT: F 233 TYR cc_start: 0.8694 (p90) cc_final: 0.7404 (p90) REVERT: F 242 MET cc_start: 0.9348 (tpp) cc_final: 0.9115 (tpp) REVERT: H 46 GLU cc_start: 0.5377 (mp0) cc_final: 0.4708 (mp0) REVERT: H 100 PHE cc_start: 0.6635 (m-80) cc_final: 0.6374 (m-10) REVERT: L 61 ARG cc_start: 0.8772 (ptp-170) cc_final: 0.8198 (ptm160) REVERT: L 69 THR cc_start: 0.7900 (m) cc_final: 0.7509 (t) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.1296 time to fit residues: 56.7975 Evaluate side-chains 228 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 8.9990 chunk 144 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS B 160 HIS B 255 GLN B 289 HIS ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.116535 restraints weight = 59990.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.118737 restraints weight = 42194.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.119330 restraints weight = 31784.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.119870 restraints weight = 25038.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.120454 restraints weight = 23485.359| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14622 Z= 0.136 Angle : 0.638 8.310 19878 Z= 0.324 Chirality : 0.046 0.205 2171 Planarity : 0.005 0.068 2525 Dihedral : 5.559 52.557 2172 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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 aren not related in a simple way. whole: -1.59 (0.19), residues: 1780 helix: -1.12 (0.65), residues: 45 sheet: -0.46 (0.20), residues: 611 loop : -1.44 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 263 TYR 0.024 0.001 TYR L 32 PHE 0.024 0.002 PHE G 241 TRP 0.031 0.002 TRP L 35 HIS 0.009 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00312 (14580) covalent geometry : angle 0.63266 (19784) SS BOND : bond 0.00285 ( 32) SS BOND : angle 1.19894 ( 64) hydrogen bonds : bond 0.03324 ( 336) hydrogen bonds : angle 6.17405 ( 861) link_BETA1-4 : bond 0.00356 ( 1) link_BETA1-4 : angle 1.06953 ( 3) link_NAG-ASN : bond 0.00269 ( 9) link_NAG-ASN : angle 1.55425 ( 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 296 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.499 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: 0.6812 (mpp) cc_final: 0.5823 (mpp) REVERT: B 81 ASP cc_start: 0.7896 (t0) cc_final: 0.7516 (t0) REVERT: B 107 GLN cc_start: 0.8347 (tp40) cc_final: 0.8061 (tp-100) REVERT: B 161 LEU cc_start: 0.8854 (mp) cc_final: 0.8581 (tt) REVERT: B 179 TYR cc_start: 0.6594 (m-80) cc_final: 0.6197 (m-80) REVERT: B 228 GLN cc_start: 0.7837 (mt0) cc_final: 0.7561 (mt0) REVERT: B 237 THR cc_start: 0.8560 (t) cc_final: 0.8291 (p) REVERT: B 333 TRP cc_start: 0.8117 (t-100) cc_final: 0.7904 (t-100) REVERT: A 46 TYR cc_start: 0.7676 (p90) cc_final: 0.7350 (p90) REVERT: A 66 LEU cc_start: 0.7326 (mm) cc_final: 0.6585 (mt) REVERT: A 97 ASP cc_start: 0.8306 (p0) cc_final: 0.7554 (p0) REVERT: A 99 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6981 (tp30) REVERT: A 187 TYR cc_start: 0.8155 (t80) cc_final: 0.7732 (t80) REVERT: A 202 ASP cc_start: 0.8146 (p0) cc_final: 0.7549 (t0) REVERT: A 217 THR cc_start: 0.8199 (p) cc_final: 0.7880 (p) REVERT: A 219 ILE cc_start: 0.8802 (tp) cc_final: 0.8312 (tp) REVERT: A 235 GLN cc_start: 0.8813 (tt0) cc_final: 0.7955 (tt0) REVERT: A 241 GLU cc_start: 0.8540 (tp30) cc_final: 0.8224 (tp30) REVERT: A 264 GLU cc_start: 0.8609 (mp0) cc_final: 0.8334 (mp0) REVERT: G 36 ASN cc_start: 0.9202 (t0) cc_final: 0.8846 (t0) REVERT: G 76 HIS cc_start: 0.7413 (p-80) cc_final: 0.6980 (p-80) REVERT: G 77 ASP cc_start: 0.7713 (m-30) cc_final: 0.7310 (p0) REVERT: G 79 LYS cc_start: 0.7490 (mppt) cc_final: 0.7213 (pttp) REVERT: G 103 PHE cc_start: 0.8426 (m-10) cc_final: 0.8011 (m-10) REVERT: G 235 ASP cc_start: 0.9301 (t0) cc_final: 0.9094 (t0) REVERT: J 59 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7817 (tm-30) REVERT: J 88 MET cc_start: 0.7673 (tpt) cc_final: 0.7461 (tpp) REVERT: J 99 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8161 (pt0) REVERT: J 233 TYR cc_start: 0.8409 (p90) cc_final: 0.7993 (p90) REVERT: K 220 MET cc_start: 0.4696 (ttt) cc_final: 0.3194 (tpt) REVERT: K 235 ASP cc_start: 0.8060 (t0) cc_final: 0.7766 (t0) REVERT: K 289 HIS cc_start: 0.8889 (m-70) cc_final: 0.8539 (m90) REVERT: F 51 PHE cc_start: 0.8318 (p90) cc_final: 0.7537 (p90) REVERT: F 233 TYR cc_start: 0.8685 (p90) cc_final: 0.7374 (p90) REVERT: F 242 MET cc_start: 0.9330 (tpp) cc_final: 0.9089 (tpp) REVERT: H 100 PHE cc_start: 0.6442 (m-80) cc_final: 0.6108 (m-80) REVERT: L 45 LYS cc_start: 0.8938 (tptp) cc_final: 0.8656 (tptp) REVERT: L 69 THR cc_start: 0.7985 (m) cc_final: 0.7600 (t) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1227 time to fit residues: 53.2478 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 : 0.551 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 0.0370 chunk 115 optimal weight: 0.8980 chunk 140 optimal weight: 0.0020 chunk 77 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 125 ASN G 275 HIS ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 336 HIS H 101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.137778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.117727 restraints weight = 60304.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.120370 restraints weight = 48994.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.121967 restraints weight = 33231.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.122423 restraints weight = 25012.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.122887 restraints weight = 23443.503| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14622 Z= 0.113 Angle : 0.617 7.934 19878 Z= 0.316 Chirality : 0.046 0.192 2171 Planarity : 0.005 0.064 2525 Dihedral : 5.380 52.322 2172 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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 aren not related in a simple way. whole: -1.49 (0.19), residues: 1780 helix: -1.20 (0.66), residues: 45 sheet: -0.38 (0.21), residues: 609 loop : -1.37 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 50 TYR 0.016 0.001 TYR A 85 PHE 0.020 0.001 PHE L 71 TRP 0.029 0.002 TRP L 35 HIS 0.007 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00264 (14580) covalent geometry : angle 0.61259 (19784) SS BOND : bond 0.00256 ( 32) SS BOND : angle 1.27705 ( 64) hydrogen bonds : bond 0.03146 ( 336) hydrogen bonds : angle 5.95729 ( 861) link_BETA1-4 : bond 0.00092 ( 1) link_BETA1-4 : angle 0.81053 ( 3) link_NAG-ASN : bond 0.00266 ( 9) link_NAG-ASN : angle 1.33480 ( 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 301 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.630 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: B 70 MET cc_start: 0.6989 (mpp) cc_final: 0.5922 (mpp) REVERT: B 81 ASP cc_start: 0.7742 (t0) cc_final: 0.7372 (t0) REVERT: B 107 GLN cc_start: 0.8441 (tp40) cc_final: 0.7873 (tp-100) REVERT: B 137 PHE cc_start: 0.9138 (p90) cc_final: 0.8424 (p90) REVERT: B 149 HIS cc_start: 0.8358 (t70) cc_final: 0.7957 (t-90) REVERT: B 179 TYR cc_start: 0.6477 (m-80) cc_final: 0.6100 (m-80) REVERT: B 228 GLN cc_start: 0.8103 (mt0) cc_final: 0.7660 (mt0) REVERT: B 237 THR cc_start: 0.8486 (t) cc_final: 0.8249 (p) REVERT: B 333 TRP cc_start: 0.8289 (t-100) cc_final: 0.8037 (t-100) REVERT: A 66 LEU cc_start: 0.7439 (mm) cc_final: 0.6701 (mt) REVERT: A 87 PHE cc_start: 0.8057 (m-10) cc_final: 0.7704 (m-10) REVERT: A 97 ASP cc_start: 0.8263 (p0) cc_final: 0.7500 (p0) REVERT: A 99 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6536 (tp30) REVERT: A 187 TYR cc_start: 0.8133 (t80) cc_final: 0.7703 (t80) REVERT: A 202 ASP cc_start: 0.8066 (p0) cc_final: 0.7508 (t0) REVERT: A 217 THR cc_start: 0.8101 (p) cc_final: 0.7865 (p) REVERT: A 219 ILE cc_start: 0.8763 (tp) cc_final: 0.8268 (tp) REVERT: A 222 LEU cc_start: 0.9435 (mt) cc_final: 0.9208 (mt) REVERT: A 235 GLN cc_start: 0.8793 (tt0) cc_final: 0.7907 (tt0) REVERT: A 241 GLU cc_start: 0.8461 (tp30) cc_final: 0.8217 (tp30) REVERT: A 264 GLU cc_start: 0.8620 (mp0) cc_final: 0.8254 (mp0) REVERT: G 36 ASN cc_start: 0.9192 (t0) cc_final: 0.8878 (t0) REVERT: G 76 HIS cc_start: 0.7362 (p-80) cc_final: 0.6944 (p-80) REVERT: G 77 ASP cc_start: 0.7716 (m-30) cc_final: 0.7266 (p0) REVERT: G 79 LYS cc_start: 0.7670 (mppt) cc_final: 0.7435 (pttp) REVERT: G 103 PHE cc_start: 0.8197 (m-10) cc_final: 0.7858 (m-10) REVERT: J 59 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7704 (tm-30) REVERT: J 99 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8140 (pt0) REVERT: J 103 LEU cc_start: 0.7704 (tp) cc_final: 0.7326 (mt) REVERT: J 233 TYR cc_start: 0.8396 (p90) cc_final: 0.8047 (p90) REVERT: K 220 MET cc_start: 0.4340 (ttt) cc_final: 0.2728 (tpt) REVERT: K 235 ASP cc_start: 0.7930 (t0) cc_final: 0.7659 (t0) REVERT: K 289 HIS cc_start: 0.8913 (m-70) cc_final: 0.8631 (m90) REVERT: K 333 TRP cc_start: 0.8494 (t-100) cc_final: 0.7821 (t-100) REVERT: K 336 HIS cc_start: 0.6502 (m90) cc_final: 0.5531 (m90) REVERT: F 51 PHE cc_start: 0.8276 (p90) cc_final: 0.7506 (p90) REVERT: F 75 ASP cc_start: 0.7890 (t0) cc_final: 0.7634 (t0) REVERT: F 216 ARG cc_start: 0.4236 (mtt180) cc_final: 0.3681 (mtt180) REVERT: F 233 TYR cc_start: 0.8623 (p90) cc_final: 0.7359 (p90) REVERT: F 242 MET cc_start: 0.9285 (tpp) cc_final: 0.9051 (tpp) REVERT: H 100 PHE cc_start: 0.6571 (m-80) cc_final: 0.6202 (m-80) REVERT: L 45 LYS cc_start: 0.8977 (tptp) cc_final: 0.8758 (tptp) REVERT: L 69 THR cc_start: 0.7935 (m) cc_final: 0.7544 (t) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1306 time to fit residues: 57.0931 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 : 0.557 ------------------------------------------------------------------------------- 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: 0.9980 chunk 154 optimal weight: 0.0470 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 G 125 ASN ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.115811 restraints weight = 59689.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.117394 restraints weight = 41200.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.118386 restraints weight = 32939.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.118959 restraints weight = 25547.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.119638 restraints weight = 24211.671| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14622 Z= 0.145 Angle : 0.645 7.795 19878 Z= 0.330 Chirality : 0.046 0.201 2171 Planarity : 0.005 0.063 2525 Dihedral : 5.510 53.556 2172 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % 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 aren not related in a simple way. whole: -1.60 (0.19), residues: 1780 helix: -1.07 (0.67), residues: 45 sheet: -0.53 (0.20), residues: 636 loop : -1.41 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.022 0.002 TYR A 46 PHE 0.024 0.002 PHE G 241 TRP 0.026 0.002 TRP L 35 HIS 0.009 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00332 (14580) covalent geometry : angle 0.63983 (19784) SS BOND : bond 0.00390 ( 32) SS BOND : angle 1.37746 ( 64) hydrogen bonds : bond 0.03230 ( 336) hydrogen bonds : angle 6.07193 ( 861) link_BETA1-4 : bond 0.00595 ( 1) link_BETA1-4 : angle 1.26265 ( 3) link_NAG-ASN : bond 0.00254 ( 9) link_NAG-ASN : angle 1.41453 ( 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 292 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.586 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 81 ASP cc_start: 0.7874 (t0) cc_final: 0.7459 (t0) REVERT: B 143 TYR cc_start: 0.8220 (p90) cc_final: 0.7721 (p90) REVERT: B 149 HIS cc_start: 0.8320 (t70) cc_final: 0.7910 (t-90) REVERT: B 228 GLN cc_start: 0.7767 (mt0) cc_final: 0.7402 (mt0) REVERT: B 237 THR cc_start: 0.8494 (t) cc_final: 0.8246 (p) REVERT: A 46 TYR cc_start: 0.7351 (p90) cc_final: 0.7053 (p90) REVERT: A 66 LEU cc_start: 0.7366 (mm) cc_final: 0.6595 (mt) REVERT: A 87 PHE cc_start: 0.8381 (m-10) cc_final: 0.8004 (m-10) REVERT: A 88 MET cc_start: 0.8935 (ttt) cc_final: 0.8674 (ppp) REVERT: A 99 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6899 (tp30) REVERT: A 187 TYR cc_start: 0.8331 (t80) cc_final: 0.7969 (t80) REVERT: A 202 ASP cc_start: 0.8155 (p0) cc_final: 0.7518 (t0) REVERT: A 219 ILE cc_start: 0.8796 (tp) cc_final: 0.8298 (tp) REVERT: A 222 LEU cc_start: 0.9386 (mt) cc_final: 0.9145 (mt) REVERT: A 228 ASN cc_start: 0.9253 (p0) cc_final: 0.8998 (p0) REVERT: A 235 GLN cc_start: 0.8938 (tt0) cc_final: 0.8076 (tt0) REVERT: A 241 GLU cc_start: 0.8491 (tp30) cc_final: 0.8250 (tp30) REVERT: A 264 GLU cc_start: 0.8682 (mp0) cc_final: 0.8388 (mp0) REVERT: G 36 ASN cc_start: 0.9179 (t0) cc_final: 0.8652 (t0) REVERT: G 76 HIS cc_start: 0.7404 (p-80) cc_final: 0.6985 (p-80) REVERT: G 77 ASP cc_start: 0.7570 (m-30) cc_final: 0.6871 (p0) REVERT: G 103 PHE cc_start: 0.8354 (m-10) cc_final: 0.7956 (m-10) REVERT: J 59 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7975 (tm-30) REVERT: J 99 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8148 (pt0) REVERT: J 103 LEU cc_start: 0.7122 (tp) cc_final: 0.6834 (mt) REVERT: J 233 TYR cc_start: 0.8504 (p90) cc_final: 0.8207 (p90) REVERT: K 220 MET cc_start: 0.4832 (ttt) cc_final: 0.3401 (tpt) REVERT: K 235 ASP cc_start: 0.8308 (t0) cc_final: 0.8100 (t0) REVERT: K 289 HIS cc_start: 0.8827 (m-70) cc_final: 0.8526 (m90) REVERT: K 333 TRP cc_start: 0.8749 (t-100) cc_final: 0.7987 (t-100) REVERT: F 51 PHE cc_start: 0.8373 (p90) cc_final: 0.7557 (p90) REVERT: F 75 ASP cc_start: 0.7992 (t0) cc_final: 0.7679 (t0) REVERT: F 233 TYR cc_start: 0.8759 (p90) cc_final: 0.7477 (p90) REVERT: F 235 GLN cc_start: 0.8219 (mm110) cc_final: 0.7957 (mm110) REVERT: F 242 MET cc_start: 0.9316 (tpp) cc_final: 0.9080 (tpp) REVERT: H 46 GLU cc_start: 0.6380 (mp0) cc_final: 0.6042 (mp0) REVERT: H 100 PHE cc_start: 0.6366 (m-80) cc_final: 0.6011 (m-80) REVERT: L 3 GLN cc_start: 0.5864 (tt0) cc_final: 0.5444 (tt0) REVERT: L 45 LYS cc_start: 0.8990 (tptp) cc_final: 0.8750 (tptp) REVERT: L 69 THR cc_start: 0.7951 (m) cc_final: 0.7642 (t) REVERT: L 76 ASN cc_start: 0.7842 (m110) cc_final: 0.7636 (m110) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.1275 time to fit residues: 54.6701 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 : 0.593 ------------------------------------------------------------------------------- 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: 3.9990 chunk 101 optimal weight: 0.0270 chunk 135 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 123 optimal weight: 0.0050 chunk 58 optimal weight: 0.8980 overall best weight: 0.5052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN B 160 HIS B 255 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN J 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.137680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.117273 restraints weight = 60268.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.119490 restraints weight = 43349.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.120855 restraints weight = 31478.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.120972 restraints weight = 24573.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.121327 restraints weight = 24639.752| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14622 Z= 0.114 Angle : 0.631 8.662 19878 Z= 0.322 Chirality : 0.046 0.189 2171 Planarity : 0.005 0.083 2525 Dihedral : 5.367 52.616 2172 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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 aren not related in a simple way. whole: -1.49 (0.19), residues: 1780 helix: -0.97 (0.67), residues: 45 sheet: -0.42 (0.21), residues: 637 loop : -1.37 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 50 TYR 0.017 0.001 TYR A 46 PHE 0.020 0.001 PHE G 262 TRP 0.029 0.002 TRP L 35 HIS 0.008 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00268 (14580) covalent geometry : angle 0.62563 (19784) SS BOND : bond 0.00317 ( 32) SS BOND : angle 1.44240 ( 64) hydrogen bonds : bond 0.03137 ( 336) hydrogen bonds : angle 5.87880 ( 861) link_BETA1-4 : bond 0.00312 ( 1) link_BETA1-4 : angle 0.88851 ( 3) link_NAG-ASN : bond 0.00265 ( 9) link_NAG-ASN : angle 1.32234 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3301.34 seconds wall clock time: 57 minutes 56.93 seconds (3476.93 seconds total)