Starting phenix.real_space_refine on Thu Jun 12 19:44:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dul_27722/06_2025/8dul_27722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dul_27722/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dul_27722/06_2025/8dul_27722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dul_27722/06_2025/8dul_27722.map" model { file = "/net/cci-nas-00/data/ceres_data/8dul_27722/06_2025/8dul_27722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dul_27722/06_2025/8dul_27722.cif" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.41, per 1000 atoms: 1.01 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: 3.17 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.97 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: 4.49 Time building geometry restraints manager: 3.84 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: 374.470 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: 0.040 Extract box with map and model: 0.810 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.480 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 418.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.002 TRP B 282 HIS 0.015 0.001 HIS B 172 PHE 0.037 0.003 PHE B 18 TYR 0.043 0.002 TYR A 85 ARG 0.030 0.001 ARG G 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 9) link_NAG-ASN : angle 4.73238 ( 27) link_BETA1-4 : bond 0.00660 ( 1) link_BETA1-4 : angle 1.50224 ( 3) hydrogen bonds : bond 0.28484 ( 336) hydrogen bonds : angle 10.36012 ( 861) SS BOND : bond 0.00430 ( 32) SS BOND : angle 1.43959 ( 64) covalent geometry : bond 0.00498 (14580) covalent geometry : angle 1.04376 (19784) *********************** 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 : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7750 (mpp) cc_final: 0.7045 (mpp) REVERT: B 228 GLN cc_start: 0.7630 (mt0) cc_final: 0.7257 (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: 0.5477 (m-30) REVERT: G 235 ASP cc_start: 0.7655 (m-30) cc_final: 0.7247 (m-30) REVERT: J 115 THR cc_start: 0.8168 (p) cc_final: 0.7884 (p) REVERT: K 56 TYR cc_start: 0.7335 (m-80) cc_final: 0.7060 (m-10) REVERT: K 220 MET cc_start: 0.0999 (ttt) cc_final: 0.0683 (tpt) REVERT: F 103 LEU cc_start: 0.7475 (tp) cc_final: 0.6908 (tt) REVERT: F 113 ASP cc_start: 0.5198 (p0) cc_final: 0.3976 (p0) REVERT: F 209 ASP cc_start: 0.6385 (p0) cc_final: 0.6138 (p0) REVERT: H 100 VAL cc_start: 0.3308 (m) cc_final: 0.2473 (m) outliers start: 1 outliers final: 1 residues processed: 459 average time/residue: 0.2985 time to fit residues: 191.7641 Evaluate side-chains 275 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 158 optimal weight: 0.1980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.145672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.126341 restraints weight = 60711.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.130127 restraints weight = 40974.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.131544 restraints weight = 26061.128| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.2487 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= 0.125 Angle : 0.642 8.971 19878 Z= 0.333 Chirality : 0.046 0.239 2171 Planarity : 0.005 0.054 2525 Dihedral : 5.881 50.916 2172 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 1780 helix: -1.59 (0.72), residues: 45 sheet: -0.47 (0.21), residues: 578 loop : -1.50 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 243 HIS 0.007 0.001 HIS K 177 PHE 0.018 0.001 PHE A 95 TYR 0.013 0.001 TYR J 85 ARG 0.008 0.001 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 9) link_NAG-ASN : angle 2.47153 ( 27) link_BETA1-4 : bond 0.00276 ( 1) link_BETA1-4 : angle 1.45263 ( 3) hydrogen bonds : bond 0.04646 ( 336) hydrogen bonds : angle 7.06949 ( 861) SS BOND : bond 0.00317 ( 32) SS BOND : angle 0.97209 ( 64) covalent geometry : bond 0.00273 (14580) covalent geometry : angle 0.63472 (19784) *********************** 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 358 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7185 (mpp) cc_final: 0.4493 (mtm) REVERT: B 81 ASP cc_start: 0.7667 (t0) cc_final: 0.7293 (t0) REVERT: B 107 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7792 (mm-40) REVERT: B 230 ILE cc_start: 0.7717 (pt) cc_final: 0.7475 (mt) REVERT: B 240 VAL cc_start: 0.9519 (m) cc_final: 0.9306 (p) REVERT: A 97 ASP cc_start: 0.8279 (p0) cc_final: 0.7710 (p0) REVERT: A 115 THR cc_start: 0.9497 (p) cc_final: 0.9280 (p) REVERT: A 118 HIS cc_start: 0.9090 (p-80) cc_final: 0.8800 (p-80) REVERT: A 217 THR cc_start: 0.8608 (p) cc_final: 0.8358 (p) REVERT: A 219 ILE cc_start: 0.8955 (tp) cc_final: 0.8472 (tp) REVERT: A 220 ARG cc_start: 0.8091 (mpp80) cc_final: 0.7555 (ptt180) REVERT: G 38 TRP cc_start: 0.8801 (m-90) cc_final: 0.8419 (m-90) REVERT: G 64 VAL cc_start: 0.8641 (p) cc_final: 0.8273 (p) REVERT: G 81 ASP cc_start: 0.7585 (m-30) cc_final: 0.7195 (m-30) REVERT: G 95 ARG cc_start: 0.8316 (tmm-80) cc_final: 0.8009 (tmm-80) REVERT: G 144 LEU cc_start: 0.9114 (mt) cc_final: 0.8497 (mt) REVERT: G 235 ASP cc_start: 0.7812 (m-30) cc_final: 0.7606 (m-30) REVERT: G 262 PHE cc_start: 0.7724 (m-80) cc_final: 0.7456 (m-10) REVERT: J 50 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8173 (ttm-80) REVERT: J 99 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7863 (pt0) REVERT: J 195 MET cc_start: 0.3182 (mmp) cc_final: 0.2726 (mmm) REVERT: J 233 TYR cc_start: 0.8519 (p90) cc_final: 0.8063 (p90) REVERT: K 38 TRP cc_start: 0.8592 (m-90) cc_final: 0.7961 (m-90) REVERT: K 220 MET cc_start: 0.3890 (ttt) cc_final: 0.3306 (tpt) REVERT: K 241 PHE cc_start: 0.8389 (t80) cc_final: 0.8096 (t80) REVERT: K 262 PHE cc_start: 0.7409 (m-80) cc_final: 0.6241 (m-10) REVERT: K 289 HIS cc_start: 0.8432 (m-70) cc_final: 0.8152 (m-70) REVERT: K 336 HIS cc_start: 0.6291 (m90) cc_final: 0.5834 (m-70) REVERT: F 51 PHE cc_start: 0.8029 (p90) cc_final: 0.7338 (p90) REVERT: F 103 LEU cc_start: 0.8249 (tp) cc_final: 0.7897 (tt) REVERT: F 117 ASP cc_start: 0.8146 (p0) cc_final: 0.7887 (t0) REVERT: F 233 TYR cc_start: 0.8444 (p90) cc_final: 0.7550 (p90) REVERT: F 242 MET cc_start: 0.9456 (tpp) cc_final: 0.9202 (tpp) REVERT: H 36 TRP cc_start: 0.6489 (m100) cc_final: 0.6131 (m-10) REVERT: H 66 ARG cc_start: -0.1371 (mmt180) cc_final: -0.3954 (ptt180) REVERT: H 96 ASP cc_start: 0.8347 (p0) cc_final: 0.7999 (p0) REVERT: L 3 GLN cc_start: 0.3743 (tt0) cc_final: 0.3385 (tt0) REVERT: L 5 THR cc_start: 0.8026 (p) cc_final: 0.7787 (p) REVERT: L 42 LYS cc_start: 0.5532 (mmmt) cc_final: 0.4805 (mmtt) REVERT: L 45 LYS cc_start: 0.8573 (tptp) cc_final: 0.8206 (tppt) REVERT: L 69 THR cc_start: 0.7725 (m) cc_final: 0.7402 (t) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.2696 time to fit residues: 137.6173 Evaluate side-chains 256 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 113 optimal weight: 0.8980 chunk 150 optimal weight: 0.0670 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 0.0470 chunk 37 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 174 optimal weight: 0.0050 overall best weight: 0.4030 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 HIS F 102 GLN F 175 HIS ** 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 = 0.4300 r_free = 0.4300 target = 0.145590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.125624 restraints weight = 60504.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.128228 restraints weight = 39074.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.130074 restraints weight = 28318.703| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14622 Z= 0.111 Angle : 0.589 7.963 19878 Z= 0.306 Chirality : 0.045 0.209 2171 Planarity : 0.005 0.050 2525 Dihedral : 5.336 50.312 2172 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), residues: 1780 helix: -1.23 (0.74), residues: 45 sheet: -0.33 (0.21), residues: 573 loop : -1.35 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 243 HIS 0.006 0.001 HIS J 175 PHE 0.012 0.001 PHE G 145 TYR 0.014 0.001 TYR L 36 ARG 0.012 0.001 ARG J 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 9) link_NAG-ASN : angle 1.51293 ( 27) link_BETA1-4 : bond 0.00475 ( 1) link_BETA1-4 : angle 1.00132 ( 3) hydrogen bonds : bond 0.03681 ( 336) hydrogen bonds : angle 6.28830 ( 861) SS BOND : bond 0.00197 ( 32) SS BOND : angle 0.89779 ( 64) covalent geometry : bond 0.00254 (14580) covalent geometry : angle 0.58551 (19784) *********************** 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 341 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.495 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 36 ASN cc_start: 0.8087 (t0) cc_final: 0.7462 (t0) REVERT: B 70 MET cc_start: 0.7368 (mpp) cc_final: 0.6540 (mpp) REVERT: B 81 ASP cc_start: 0.7632 (t0) cc_final: 0.7252 (t0) REVERT: B 333 TRP cc_start: 0.8079 (t-100) cc_final: 0.7592 (t-100) REVERT: A 97 ASP cc_start: 0.8323 (p0) cc_final: 0.7752 (p0) REVERT: A 99 GLU cc_start: 0.7135 (tp30) cc_final: 0.6660 (mm-30) REVERT: A 115 THR cc_start: 0.9616 (p) cc_final: 0.9341 (p) REVERT: A 118 HIS cc_start: 0.9191 (p-80) cc_final: 0.8811 (p-80) REVERT: A 202 ASP cc_start: 0.8031 (p0) cc_final: 0.7343 (t70) REVERT: A 219 ILE cc_start: 0.9039 (tp) cc_final: 0.8681 (tp) REVERT: A 220 ARG cc_start: 0.8002 (mpp80) cc_final: 0.7616 (ptt-90) REVERT: A 241 GLU cc_start: 0.8594 (tp30) cc_final: 0.8205 (tp30) REVERT: G 38 TRP cc_start: 0.8921 (m-90) cc_final: 0.8565 (m-90) REVERT: G 49 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6634 (tm-30) REVERT: G 64 VAL cc_start: 0.8654 (p) cc_final: 0.8299 (p) REVERT: G 95 ARG cc_start: 0.8322 (tmm-80) cc_final: 0.7958 (tmm-80) REVERT: G 235 ASP cc_start: 0.7593 (m-30) cc_final: 0.7353 (m-30) REVERT: J 99 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7880 (pt0) REVERT: J 233 TYR cc_start: 0.8591 (p90) cc_final: 0.8245 (p90) REVERT: K 23 ARG cc_start: 0.8521 (ptt90) cc_final: 0.7799 (tmm-80) REVERT: K 143 TYR cc_start: 0.8323 (p90) cc_final: 0.8022 (p90) REVERT: K 336 HIS cc_start: 0.5961 (m90) cc_final: 0.5714 (m-70) REVERT: F 51 PHE cc_start: 0.7966 (p90) cc_final: 0.7028 (p90) REVERT: F 103 LEU cc_start: 0.8312 (tp) cc_final: 0.7946 (tt) REVERT: F 233 TYR cc_start: 0.8381 (p90) cc_final: 0.7287 (p90) REVERT: F 234 THR cc_start: 0.7774 (p) cc_final: 0.6769 (p) REVERT: F 235 GLN cc_start: 0.6989 (mm110) cc_final: 0.5810 (tp40) REVERT: F 242 MET cc_start: 0.9418 (tpp) cc_final: 0.9205 (tpp) REVERT: H 36 TRP cc_start: 0.6349 (m100) cc_final: 0.6019 (m-10) REVERT: H 66 ARG cc_start: -0.1205 (mmt180) cc_final: -0.2297 (mmm160) REVERT: H 96 ASP cc_start: 0.8325 (p0) cc_final: 0.8022 (p0) REVERT: H 100 PHE cc_start: 0.7603 (m-10) cc_final: 0.7235 (m-80) REVERT: L 45 LYS cc_start: 0.8365 (tptp) cc_final: 0.8158 (tppt) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2747 time to fit residues: 132.5219 Evaluate side-chains 252 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 137 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS A 235 GLN G 255 GLN ** J 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN F 100 ASN ** L 90 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 = 0.4116 r_free = 0.4116 target = 0.132294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.113382 restraints weight = 55927.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.113688 restraints weight = 36542.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.114321 restraints weight = 29816.404| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 14622 Z= 0.293 Angle : 0.863 12.062 19878 Z= 0.445 Chirality : 0.049 0.204 2171 Planarity : 0.008 0.091 2525 Dihedral : 6.627 55.656 2172 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.26 % Allowed : 7.06 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.18), residues: 1780 helix: -1.35 (0.67), residues: 45 sheet: -0.66 (0.20), residues: 585 loop : -1.52 (0.16), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP F 243 HIS 0.014 0.002 HIS B 289 PHE 0.040 0.003 PHE J 170 TYR 0.032 0.002 TYR J 185 ARG 0.038 0.002 ARG K 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 9) link_NAG-ASN : angle 2.69151 ( 27) link_BETA1-4 : bond 0.00471 ( 1) link_BETA1-4 : angle 1.43200 ( 3) hydrogen bonds : bond 0.04418 ( 336) hydrogen bonds : angle 7.31102 ( 861) SS BOND : bond 0.00523 ( 32) SS BOND : angle 1.29985 ( 64) covalent geometry : bond 0.00620 (14580) covalent geometry : angle 0.85618 (19784) *********************** 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 314 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 310 time to evaluate : 1.725 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 16 LEU cc_start: 0.8331 (pt) cc_final: 0.7833 (tt) REVERT: B 70 MET cc_start: 0.7693 (mpp) cc_final: 0.6625 (mpp) REVERT: B 81 ASP cc_start: 0.8061 (t0) cc_final: 0.7779 (t0) REVERT: B 102 TYR cc_start: 0.8173 (m-80) cc_final: 0.7868 (m-80) REVERT: B 107 GLN cc_start: 0.8635 (tp40) cc_final: 0.8058 (tp-100) REVERT: B 333 TRP cc_start: 0.8163 (t-100) cc_final: 0.7778 (t-100) REVERT: A 50 ARG cc_start: 0.8964 (tpp80) cc_final: 0.8696 (tpp80) REVERT: A 66 LEU cc_start: 0.7493 (mm) cc_final: 0.6652 (mt) REVERT: A 97 ASP cc_start: 0.8267 (p0) cc_final: 0.7688 (p0) REVERT: A 109 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 124 VAL cc_start: 0.7308 (OUTLIER) cc_final: 0.7032 (t) REVERT: A 187 TYR cc_start: 0.7888 (t80) cc_final: 0.7386 (t80) REVERT: A 195 MET cc_start: 0.8315 (mmm) cc_final: 0.7747 (mmm) REVERT: A 202 ASP cc_start: 0.8093 (p0) cc_final: 0.7632 (t70) REVERT: A 241 GLU cc_start: 0.8828 (tp30) cc_final: 0.8486 (tp30) REVERT: G 36 ASN cc_start: 0.8784 (t0) cc_final: 0.8216 (t0) REVERT: G 79 LYS cc_start: 0.7424 (mppt) cc_final: 0.7189 (pttm) REVERT: G 95 ARG cc_start: 0.8724 (tmm-80) cc_final: 0.8465 (tmm-80) REVERT: G 144 LEU cc_start: 0.9033 (mt) cc_final: 0.8809 (mt) REVERT: J 241 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8542 (mp0) REVERT: K 289 HIS cc_start: 0.9115 (m-70) cc_final: 0.8749 (m90) REVERT: K 297 LEU cc_start: 0.9044 (tp) cc_final: 0.8441 (tp) REVERT: K 313 TRP cc_start: 0.9305 (m100) cc_final: 0.9080 (m100) REVERT: K 336 HIS cc_start: 0.6371 (m90) cc_final: 0.5752 (m-70) REVERT: F 51 PHE cc_start: 0.8469 (p90) cc_final: 0.7566 (p90) REVERT: F 233 TYR cc_start: 0.8820 (p90) cc_final: 0.7157 (p90) REVERT: F 235 GLN cc_start: 0.8270 (mm110) cc_final: 0.7634 (mm110) REVERT: F 242 MET cc_start: 0.9392 (tpp) cc_final: 0.9178 (tpp) REVERT: H 100 PHE cc_start: 0.7761 (m-10) cc_final: 0.7445 (m-10) outliers start: 4 outliers final: 1 residues processed: 314 average time/residue: 0.2844 time to fit residues: 127.0796 Evaluate side-chains 216 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 106 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN A 59 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.129837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.110288 restraints weight = 55008.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.110913 restraints weight = 37166.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.111603 restraints weight = 30262.414| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14622 Z= 0.262 Angle : 0.790 12.322 19878 Z= 0.406 Chirality : 0.048 0.232 2171 Planarity : 0.006 0.054 2525 Dihedral : 6.534 53.112 2172 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.18), residues: 1780 helix: -1.31 (0.67), residues: 45 sheet: -0.94 (0.19), residues: 642 loop : -1.57 (0.17), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 342 HIS 0.011 0.002 HIS B 156 PHE 0.032 0.003 PHE J 170 TYR 0.022 0.002 TYR L 49 ARG 0.026 0.001 ARG F 267 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 9) link_NAG-ASN : angle 2.26414 ( 27) link_BETA1-4 : bond 0.00034 ( 1) link_BETA1-4 : angle 0.58882 ( 3) hydrogen bonds : bond 0.03991 ( 336) hydrogen bonds : angle 7.20260 ( 861) SS BOND : bond 0.00422 ( 32) SS BOND : angle 1.28133 ( 64) covalent geometry : bond 0.00557 (14580) covalent geometry : angle 0.78441 (19784) *********************** 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 305 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.600 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 81 ASP cc_start: 0.8126 (t0) cc_final: 0.7910 (t0) REVERT: B 102 TYR cc_start: 0.7938 (m-80) cc_final: 0.7588 (m-80) REVERT: B 107 GLN cc_start: 0.8267 (tp40) cc_final: 0.7650 (mm-40) REVERT: B 228 GLN cc_start: 0.7365 (mt0) cc_final: 0.6998 (mt0) REVERT: A 50 ARG cc_start: 0.9064 (tpp80) cc_final: 0.8804 (tpp80) REVERT: A 66 LEU cc_start: 0.7544 (mm) cc_final: 0.6653 (mt) REVERT: A 97 ASP cc_start: 0.8376 (p0) cc_final: 0.7866 (p0) REVERT: A 99 GLU cc_start: 0.7702 (tp30) cc_final: 0.7383 (tp30) REVERT: A 187 TYR cc_start: 0.8084 (t80) cc_final: 0.7690 (t80) REVERT: A 202 ASP cc_start: 0.7879 (p0) cc_final: 0.7350 (t70) REVERT: A 220 ARG cc_start: 0.7546 (mpp80) cc_final: 0.6603 (mpp80) REVERT: A 222 LEU cc_start: 0.9407 (mt) cc_final: 0.9189 (mt) REVERT: A 241 GLU cc_start: 0.8648 (tp30) cc_final: 0.8376 (tp30) REVERT: A 264 GLU cc_start: 0.8814 (mp0) cc_final: 0.8555 (mp0) REVERT: G 36 ASN cc_start: 0.9097 (t0) cc_final: 0.8698 (t0) REVERT: G 79 LYS cc_start: 0.7925 (mppt) cc_final: 0.7573 (pttm) REVERT: G 95 ARG cc_start: 0.8691 (tmm-80) cc_final: 0.8297 (tmm-80) REVERT: J 62 CYS cc_start: 0.7048 (m) cc_final: 0.6839 (m) REVERT: J 233 TYR cc_start: 0.8461 (p90) cc_final: 0.8122 (p90) REVERT: J 241 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8601 (mp0) REVERT: K 154 LYS cc_start: 0.8105 (tptt) cc_final: 0.7869 (tptp) REVERT: K 220 MET cc_start: 0.4864 (ttt) cc_final: 0.3554 (tpt) REVERT: K 313 TRP cc_start: 0.9293 (m100) cc_final: 0.9029 (m100) REVERT: K 336 HIS cc_start: 0.6661 (m90) cc_final: 0.5992 (m90) REVERT: F 50 ARG cc_start: 0.8305 (ttp80) cc_final: 0.8014 (ttp80) REVERT: F 51 PHE cc_start: 0.8582 (p90) cc_final: 0.7645 (p90) REVERT: F 216 ARG cc_start: 0.4280 (mtt180) cc_final: 0.3971 (mtt180) REVERT: F 233 TYR cc_start: 0.8980 (p90) cc_final: 0.7692 (p90) REVERT: F 242 MET cc_start: 0.9289 (tpp) cc_final: 0.9057 (tpp) REVERT: F 264 GLU cc_start: 0.9042 (pp20) cc_final: 0.8701 (pp20) REVERT: H 46 GLU cc_start: 0.5151 (mp0) cc_final: 0.4358 (mp0) REVERT: H 100 PHE cc_start: 0.7871 (m-10) cc_final: 0.7666 (m-10) REVERT: L 4 MET cc_start: 0.6371 (mmm) cc_final: 0.6149 (mmm) REVERT: L 36 TYR cc_start: 0.6823 (m-80) cc_final: 0.6382 (m-80) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2777 time to fit residues: 122.0288 Evaluate side-chains 222 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 119 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN J 102 GLN J 204 GLN ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 HIS K 125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.135302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.115570 restraints weight = 62058.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.117062 restraints weight = 42010.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.117976 restraints weight = 33275.290| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14622 Z= 0.138 Angle : 0.659 7.111 19878 Z= 0.336 Chirality : 0.047 0.227 2171 Planarity : 0.005 0.059 2525 Dihedral : 5.931 53.290 2172 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.19), residues: 1780 helix: -1.08 (0.68), residues: 45 sheet: -0.88 (0.19), residues: 658 loop : -1.41 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.006 0.001 HIS J 230 PHE 0.016 0.002 PHE A 95 TYR 0.016 0.001 TYR L 86 ARG 0.006 0.001 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 9) link_NAG-ASN : angle 1.77087 ( 27) link_BETA1-4 : bond 0.00332 ( 1) link_BETA1-4 : angle 0.88584 ( 3) hydrogen bonds : bond 0.03352 ( 336) hydrogen bonds : angle 6.65927 ( 861) SS BOND : bond 0.00317 ( 32) SS BOND : angle 1.23109 ( 64) covalent geometry : bond 0.00307 (14580) covalent geometry : angle 0.65331 (19784) *********************** 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 315 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.749 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: 0.7507 (mpp) cc_final: 0.6662 (mpp) REVERT: B 81 ASP cc_start: 0.8143 (t0) cc_final: 0.7725 (t0) REVERT: B 102 TYR cc_start: 0.7869 (m-80) cc_final: 0.7570 (m-80) REVERT: B 107 GLN cc_start: 0.8062 (tp40) cc_final: 0.7607 (tp40) REVERT: B 237 THR cc_start: 0.8379 (t) cc_final: 0.8079 (p) REVERT: A 50 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8762 (tpp80) REVERT: A 66 LEU cc_start: 0.7241 (mm) cc_final: 0.6285 (mt) REVERT: A 87 PHE cc_start: 0.8446 (m-10) cc_final: 0.8232 (m-10) REVERT: A 97 ASP cc_start: 0.8398 (p0) cc_final: 0.7847 (p0) REVERT: A 109 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 187 TYR cc_start: 0.8197 (t80) cc_final: 0.7797 (t80) REVERT: A 241 GLU cc_start: 0.8467 (tp30) cc_final: 0.8178 (tp30) REVERT: A 264 GLU cc_start: 0.8728 (mp0) cc_final: 0.8382 (mp0) REVERT: G 36 ASN cc_start: 0.9201 (t0) cc_final: 0.8710 (t0) REVERT: G 95 ARG cc_start: 0.8710 (tmm-80) cc_final: 0.8278 (tmm-80) REVERT: G 169 ILE cc_start: 0.9439 (mm) cc_final: 0.9239 (tp) REVERT: J 59 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8091 (tm-30) REVERT: J 62 CYS cc_start: 0.6980 (m) cc_final: 0.6752 (m) REVERT: J 233 TYR cc_start: 0.8346 (p90) cc_final: 0.8002 (p90) REVERT: J 241 GLU cc_start: 0.8703 (mm-30) cc_final: 0.7508 (mm-30) REVERT: K 154 LYS cc_start: 0.8176 (tptt) cc_final: 0.7921 (tptp) REVERT: K 220 MET cc_start: 0.4604 (ttt) cc_final: 0.3113 (tpt) REVERT: K 240 VAL cc_start: 0.9082 (t) cc_final: 0.8859 (p) REVERT: K 289 HIS cc_start: 0.8840 (m-70) cc_final: 0.8501 (m90) REVERT: K 336 HIS cc_start: 0.6430 (m90) cc_final: 0.5800 (m90) REVERT: F 51 PHE cc_start: 0.8437 (p90) cc_final: 0.7534 (p90) REVERT: F 233 TYR cc_start: 0.8947 (p90) cc_final: 0.7694 (p90) REVERT: F 242 MET cc_start: 0.9246 (tpp) cc_final: 0.9013 (tpp) REVERT: H 77 THR cc_start: 0.6060 (p) cc_final: 0.5815 (p) REVERT: H 100 PHE cc_start: 0.7548 (m-10) cc_final: 0.7197 (m-10) REVERT: L 36 TYR cc_start: 0.6707 (m-80) cc_final: 0.6324 (m-80) REVERT: L 61 ARG cc_start: 0.8723 (ptp-170) cc_final: 0.8080 (ptm160) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2882 time to fit residues: 128.7961 Evaluate side-chains 238 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 124 optimal weight: 0.0030 chunk 76 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4748 ------------------------------------------------------------------------------- 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 ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.136917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.116969 restraints weight = 61565.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.119171 restraints weight = 42823.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.119741 restraints weight = 34274.035| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14622 Z= 0.115 Angle : 0.631 7.223 19878 Z= 0.322 Chirality : 0.046 0.208 2171 Planarity : 0.005 0.050 2525 Dihedral : 5.588 52.502 2172 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.19), residues: 1780 helix: -1.08 (0.67), residues: 45 sheet: -0.77 (0.19), residues: 654 loop : -1.34 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 103 HIS 0.005 0.001 HIS A 230 PHE 0.013 0.001 PHE A 95 TYR 0.019 0.001 TYR A 46 ARG 0.011 0.001 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 9) link_NAG-ASN : angle 1.45285 ( 27) link_BETA1-4 : bond 0.00432 ( 1) link_BETA1-4 : angle 0.92492 ( 3) hydrogen bonds : bond 0.03128 ( 336) hydrogen bonds : angle 6.26690 ( 861) SS BOND : bond 0.00344 ( 32) SS BOND : angle 1.07838 ( 64) covalent geometry : bond 0.00266 (14580) covalent geometry : angle 0.62758 (19784) *********************** 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 313 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7535 (mpp) cc_final: 0.6621 (mpp) REVERT: B 81 ASP cc_start: 0.8087 (t0) cc_final: 0.7652 (t0) REVERT: B 102 TYR cc_start: 0.7801 (m-80) cc_final: 0.6979 (m-80) REVERT: B 237 THR cc_start: 0.8513 (t) cc_final: 0.8277 (p) REVERT: A 50 ARG cc_start: 0.9114 (tpp80) cc_final: 0.8748 (tpp80) REVERT: A 66 LEU cc_start: 0.7280 (mm) cc_final: 0.6309 (mt) REVERT: A 87 PHE cc_start: 0.8365 (m-10) cc_final: 0.8110 (m-10) REVERT: A 97 ASP cc_start: 0.8283 (p0) cc_final: 0.7695 (p0) REVERT: A 99 GLU cc_start: 0.7665 (tp30) cc_final: 0.7423 (tp30) REVERT: A 109 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 187 TYR cc_start: 0.8146 (t80) cc_final: 0.7756 (t80) REVERT: A 241 GLU cc_start: 0.8528 (tp30) cc_final: 0.8123 (tp30) REVERT: A 264 GLU cc_start: 0.8715 (mp0) cc_final: 0.8336 (mp0) REVERT: G 36 ASN cc_start: 0.8938 (t0) cc_final: 0.8511 (t0) REVERT: G 76 HIS cc_start: 0.7441 (p-80) cc_final: 0.7113 (p-80) REVERT: G 77 ASP cc_start: 0.8273 (m-30) cc_final: 0.7487 (p0) REVERT: G 169 ILE cc_start: 0.9293 (mm) cc_final: 0.9065 (tp) REVERT: G 171 MET cc_start: 0.8086 (mpp) cc_final: 0.7614 (mpp) REVERT: J 59 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7741 (tm-30) REVERT: J 62 CYS cc_start: 0.7025 (m) cc_final: 0.6782 (m) REVERT: J 233 TYR cc_start: 0.8244 (p90) cc_final: 0.7935 (p90) REVERT: K 154 LYS cc_start: 0.8191 (tptt) cc_final: 0.7937 (tptp) REVERT: K 220 MET cc_start: 0.4617 (ttt) cc_final: 0.3059 (tpt) REVERT: K 240 VAL cc_start: 0.9040 (t) cc_final: 0.8787 (p) REVERT: K 264 LEU cc_start: 0.8731 (mt) cc_final: 0.8474 (mt) REVERT: K 289 HIS cc_start: 0.8757 (m-70) cc_final: 0.8437 (m90) REVERT: K 336 HIS cc_start: 0.6188 (m90) cc_final: 0.5586 (m90) REVERT: F 51 PHE cc_start: 0.8326 (p90) cc_final: 0.7499 (p90) REVERT: F 233 TYR cc_start: 0.8875 (p90) cc_final: 0.7886 (p90) REVERT: F 242 MET cc_start: 0.9167 (tpp) cc_final: 0.8934 (tpp) REVERT: H 77 THR cc_start: 0.5869 (p) cc_final: 0.5648 (p) REVERT: H 100 PHE cc_start: 0.7471 (m-10) cc_final: 0.6990 (m-10) REVERT: L 3 GLN cc_start: -0.0811 (pt0) cc_final: -0.1233 (tt0) REVERT: L 4 MET cc_start: 0.6238 (mmm) cc_final: 0.5975 (mmm) REVERT: L 61 ARG cc_start: 0.8730 (ptp-170) cc_final: 0.8108 (ptm160) REVERT: L 89 LEU cc_start: 0.8490 (tp) cc_final: 0.8170 (tp) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.2771 time to fit residues: 123.4806 Evaluate side-chains 247 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN K 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.131334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.112124 restraints weight = 58117.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.112673 restraints weight = 40635.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.114123 restraints weight = 30581.072| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.6136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14622 Z= 0.212 Angle : 0.720 9.723 19878 Z= 0.367 Chirality : 0.047 0.311 2171 Planarity : 0.006 0.069 2525 Dihedral : 6.001 54.613 2172 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1780 helix: -1.16 (0.69), residues: 45 sheet: -0.87 (0.19), residues: 648 loop : -1.39 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 342 HIS 0.011 0.002 HIS J 175 PHE 0.023 0.002 PHE J 170 TYR 0.016 0.002 TYR J 185 ARG 0.010 0.001 ARG H 100B Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 9) link_NAG-ASN : angle 1.88125 ( 27) link_BETA1-4 : bond 0.00244 ( 1) link_BETA1-4 : angle 1.23268 ( 3) hydrogen bonds : bond 0.03471 ( 336) hydrogen bonds : angle 6.69221 ( 861) SS BOND : bond 0.00280 ( 32) SS BOND : angle 1.16401 ( 64) covalent geometry : bond 0.00468 (14580) covalent geometry : angle 0.71518 (19784) *********************** 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 301 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.572 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 16 LEU cc_start: 0.8464 (pt) cc_final: 0.8237 (pt) REVERT: B 70 MET cc_start: 0.7125 (mpp) cc_final: 0.6557 (mpp) REVERT: B 237 THR cc_start: 0.8533 (t) cc_final: 0.8199 (p) REVERT: A 50 ARG cc_start: 0.9037 (tpp80) cc_final: 0.8745 (tpp80) REVERT: A 66 LEU cc_start: 0.7337 (mm) cc_final: 0.6378 (mt) REVERT: A 87 PHE cc_start: 0.8249 (m-10) cc_final: 0.8012 (m-10) REVERT: A 97 ASP cc_start: 0.8190 (p0) cc_final: 0.7620 (p0) REVERT: A 241 GLU cc_start: 0.8764 (tp30) cc_final: 0.8365 (tp30) REVERT: A 264 GLU cc_start: 0.8793 (mp0) cc_final: 0.8398 (mp0) REVERT: G 36 ASN cc_start: 0.8836 (t0) cc_final: 0.8115 (t0) REVERT: G 76 HIS cc_start: 0.7684 (p-80) cc_final: 0.7331 (p-80) REVERT: G 77 ASP cc_start: 0.8309 (m-30) cc_final: 0.7704 (p0) REVERT: G 79 LYS cc_start: 0.7758 (mppt) cc_final: 0.7299 (pttm) REVERT: G 163 GLU cc_start: 0.8787 (mp0) cc_final: 0.8343 (mp0) REVERT: J 59 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8193 (tm-30) REVERT: J 233 TYR cc_start: 0.8386 (p90) cc_final: 0.8153 (p90) REVERT: K 154 LYS cc_start: 0.8202 (tptt) cc_final: 0.7955 (tptp) REVERT: K 220 MET cc_start: 0.4909 (ttt) cc_final: 0.3467 (tpt) REVERT: K 297 LEU cc_start: 0.9158 (tp) cc_final: 0.8425 (tp) REVERT: K 333 TRP cc_start: 0.8865 (t-100) cc_final: 0.7778 (t-100) REVERT: K 336 HIS cc_start: 0.6679 (m90) cc_final: 0.5788 (m90) REVERT: F 51 PHE cc_start: 0.8458 (p90) cc_final: 0.7558 (p90) REVERT: F 216 ARG cc_start: 0.4376 (mtt180) cc_final: 0.3884 (mtt180) REVERT: F 233 TYR cc_start: 0.9123 (p90) cc_final: 0.8067 (p90) REVERT: F 235 GLN cc_start: 0.8327 (mm110) cc_final: 0.8113 (mm110) REVERT: F 242 MET cc_start: 0.9323 (tpp) cc_final: 0.9107 (tpp) REVERT: H 77 THR cc_start: 0.5836 (p) cc_final: 0.5578 (p) REVERT: H 100 PHE cc_start: 0.7662 (m-10) cc_final: 0.7339 (m-10) REVERT: L 36 TYR cc_start: 0.6771 (m-80) cc_final: 0.6538 (m-80) REVERT: L 61 ARG cc_start: 0.8705 (ptp-170) cc_final: 0.8123 (ptm160) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2776 time to fit residues: 119.2162 Evaluate side-chains 232 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 123 optimal weight: 0.0020 chunk 42 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.114663 restraints weight = 59571.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.115692 restraints weight = 45302.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.117239 restraints weight = 33591.614| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14622 Z= 0.125 Angle : 0.659 8.193 19878 Z= 0.336 Chirality : 0.047 0.259 2171 Planarity : 0.005 0.062 2525 Dihedral : 5.672 52.853 2172 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1780 helix: -1.13 (0.68), residues: 45 sheet: -0.77 (0.20), residues: 629 loop : -1.24 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 313 HIS 0.010 0.001 HIS J 175 PHE 0.016 0.001 PHE J 87 TYR 0.022 0.001 TYR A 46 ARG 0.011 0.001 ARG F 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 9) link_NAG-ASN : angle 1.52138 ( 27) link_BETA1-4 : bond 0.00397 ( 1) link_BETA1-4 : angle 0.83103 ( 3) hydrogen bonds : bond 0.03242 ( 336) hydrogen bonds : angle 6.41860 ( 861) SS BOND : bond 0.00333 ( 32) SS BOND : angle 1.11920 ( 64) covalent geometry : bond 0.00287 (14580) covalent geometry : angle 0.65498 (19784) *********************** 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 305 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 MET cc_start: 0.7486 (mpp) cc_final: 0.6482 (mpp) REVERT: B 102 TYR cc_start: 0.8092 (m-80) cc_final: 0.7722 (m-10) REVERT: B 107 GLN cc_start: 0.8482 (mm-40) cc_final: 0.7892 (mm-40) REVERT: B 135 ARG cc_start: 0.9279 (ttm110) cc_final: 0.9065 (ttm110) REVERT: B 179 TYR cc_start: 0.7112 (m-80) cc_final: 0.6499 (m-80) REVERT: B 237 THR cc_start: 0.8481 (t) cc_final: 0.8214 (p) REVERT: A 50 ARG cc_start: 0.9102 (tpp80) cc_final: 0.8735 (tpp80) REVERT: A 66 LEU cc_start: 0.7178 (mm) cc_final: 0.6123 (mt) REVERT: A 87 PHE cc_start: 0.8284 (m-10) cc_final: 0.8020 (m-10) REVERT: A 97 ASP cc_start: 0.8298 (p0) cc_final: 0.7689 (p0) REVERT: A 187 TYR cc_start: 0.8332 (t80) cc_final: 0.8042 (t80) REVERT: A 241 GLU cc_start: 0.8508 (tp30) cc_final: 0.8097 (tp30) REVERT: A 264 GLU cc_start: 0.8860 (mp0) cc_final: 0.8407 (mp0) REVERT: G 36 ASN cc_start: 0.9006 (t0) cc_final: 0.8209 (t0) REVERT: G 49 GLN cc_start: 0.5973 (tm-30) cc_final: 0.5429 (tm-30) REVERT: G 68 ARG cc_start: 0.5914 (mmt180) cc_final: 0.5580 (mtt-85) REVERT: G 76 HIS cc_start: 0.7647 (p-80) cc_final: 0.7199 (p-80) REVERT: G 77 ASP cc_start: 0.7795 (m-30) cc_final: 0.7443 (p0) REVERT: G 79 LYS cc_start: 0.7426 (mppt) cc_final: 0.7020 (pttm) REVERT: J 59 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7934 (tm-30) REVERT: J 62 CYS cc_start: 0.7223 (m) cc_final: 0.6917 (m) REVERT: J 233 TYR cc_start: 0.8343 (p90) cc_final: 0.8032 (p90) REVERT: K 154 LYS cc_start: 0.8187 (tptt) cc_final: 0.7963 (tptp) REVERT: K 220 MET cc_start: 0.5059 (ttt) cc_final: 0.3733 (tpt) REVERT: K 289 HIS cc_start: 0.8816 (m-70) cc_final: 0.8528 (m90) REVERT: K 333 TRP cc_start: 0.8556 (t-100) cc_final: 0.7697 (t-100) REVERT: K 336 HIS cc_start: 0.6479 (m90) cc_final: 0.5577 (m90) REVERT: F 51 PHE cc_start: 0.8364 (p90) cc_final: 0.7459 (p90) REVERT: F 195 MET cc_start: 0.8158 (ttt) cc_final: 0.7756 (ttt) REVERT: F 233 TYR cc_start: 0.8951 (p90) cc_final: 0.8070 (p90) REVERT: F 242 MET cc_start: 0.9139 (tpp) cc_final: 0.8914 (tpp) REVERT: H 46 GLU cc_start: 0.5647 (mp0) cc_final: 0.5336 (mp0) REVERT: H 77 THR cc_start: 0.6284 (p) cc_final: 0.5373 (p) REVERT: H 100 PHE cc_start: 0.7206 (m-10) cc_final: 0.6729 (m-10) REVERT: L 36 TYR cc_start: 0.6624 (m-80) cc_final: 0.6243 (m-80) REVERT: L 61 ARG cc_start: 0.8681 (ptp-170) cc_final: 0.8229 (ptm160) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2770 time to fit residues: 120.8335 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 : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 159 optimal weight: 0.5980 chunk 162 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN G 275 HIS ** K 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.135453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.114738 restraints weight = 59414.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.116933 restraints weight = 41475.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.117997 restraints weight = 30713.352| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14622 Z= 0.125 Angle : 0.648 8.311 19878 Z= 0.329 Chirality : 0.046 0.241 2171 Planarity : 0.005 0.082 2525 Dihedral : 5.552 53.118 2172 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.19), residues: 1780 helix: -1.08 (0.68), residues: 45 sheet: -0.78 (0.20), residues: 654 loop : -1.27 (0.18), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 103 HIS 0.011 0.001 HIS J 230 PHE 0.039 0.002 PHE J 87 TYR 0.014 0.001 TYR A 46 ARG 0.007 0.001 ARG F 249 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 9) link_NAG-ASN : angle 1.42302 ( 27) link_BETA1-4 : bond 0.00241 ( 1) link_BETA1-4 : angle 0.95856 ( 3) hydrogen bonds : bond 0.03165 ( 336) hydrogen bonds : angle 6.27728 ( 861) SS BOND : bond 0.00245 ( 32) SS BOND : angle 1.09096 ( 64) covalent geometry : bond 0.00292 (14580) covalent geometry : angle 0.64469 (19784) ********************** 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 304 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.856 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: 0.7850 (mpp) cc_final: 0.6686 (mpp) REVERT: B 102 TYR cc_start: 0.8024 (m-80) cc_final: 0.7244 (m-10) REVERT: B 135 ARG cc_start: 0.9311 (ttm110) cc_final: 0.8943 (ttm110) REVERT: B 179 TYR cc_start: 0.7080 (m-80) cc_final: 0.6461 (m-80) REVERT: B 237 THR cc_start: 0.8564 (t) cc_final: 0.8262 (p) REVERT: A 50 ARG cc_start: 0.9085 (tpp80) cc_final: 0.8754 (tpp80) REVERT: A 66 LEU cc_start: 0.7286 (mm) cc_final: 0.6234 (mt) REVERT: A 87 PHE cc_start: 0.8126 (m-10) cc_final: 0.7886 (m-10) REVERT: A 97 ASP cc_start: 0.8289 (p0) cc_final: 0.7641 (p0) REVERT: A 110 PHE cc_start: 0.6771 (m-10) cc_final: 0.5992 (m-10) REVERT: A 241 GLU cc_start: 0.8503 (tp30) cc_final: 0.8088 (tp30) REVERT: A 264 GLU cc_start: 0.8730 (mp0) cc_final: 0.8270 (mp0) REVERT: G 36 ASN cc_start: 0.9022 (t0) cc_final: 0.8301 (t0) REVERT: G 49 GLN cc_start: 0.5924 (tm-30) cc_final: 0.5349 (tm-30) REVERT: G 76 HIS cc_start: 0.7464 (p-80) cc_final: 0.7032 (p-80) REVERT: G 77 ASP cc_start: 0.7869 (m-30) cc_final: 0.7218 (p0) REVERT: J 59 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8158 (tm-30) REVERT: J 60 VAL cc_start: 0.8488 (t) cc_final: 0.8256 (t) REVERT: J 62 CYS cc_start: 0.7129 (m) cc_final: 0.6876 (m) REVERT: J 233 TYR cc_start: 0.8333 (p90) cc_final: 0.8010 (p90) REVERT: K 154 LYS cc_start: 0.8236 (tptt) cc_final: 0.8005 (tptp) REVERT: K 220 MET cc_start: 0.4914 (ttt) cc_final: 0.3496 (tpt) REVERT: K 289 HIS cc_start: 0.8691 (m-70) cc_final: 0.8426 (m90) REVERT: K 333 TRP cc_start: 0.8609 (t-100) cc_final: 0.8111 (t-100) REVERT: K 336 HIS cc_start: 0.6565 (m90) cc_final: 0.6122 (m90) REVERT: F 51 PHE cc_start: 0.8317 (p90) cc_final: 0.7487 (p90) REVERT: F 233 TYR cc_start: 0.8982 (p90) cc_final: 0.8102 (p90) REVERT: F 242 MET cc_start: 0.9176 (tpp) cc_final: 0.8962 (tpp) REVERT: H 46 GLU cc_start: 0.5673 (mp0) cc_final: 0.5385 (mp0) REVERT: H 100 PHE cc_start: 0.7434 (m-10) cc_final: 0.7176 (m-10) REVERT: L 61 ARG cc_start: 0.8713 (ptp-170) cc_final: 0.8243 (ptm160) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2643 time to fit residues: 115.6619 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 : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 108 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 124 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 156 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.135412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.115156 restraints weight = 61209.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.117109 restraints weight = 42056.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.118087 restraints weight = 32331.014| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14622 Z= 0.124 Angle : 0.649 8.484 19878 Z= 0.329 Chirality : 0.046 0.237 2171 Planarity : 0.005 0.058 2525 Dihedral : 5.485 52.986 2172 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1780 helix: -1.14 (0.68), residues: 45 sheet: -0.75 (0.20), residues: 618 loop : -1.24 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 103 HIS 0.010 0.001 HIS J 175 PHE 0.024 0.002 PHE J 87 TYR 0.024 0.001 TYR A 46 ARG 0.011 0.001 ARG B 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 9) link_NAG-ASN : angle 1.35639 ( 27) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 0.97012 ( 3) hydrogen bonds : bond 0.03190 ( 336) hydrogen bonds : angle 6.24590 ( 861) SS BOND : bond 0.00248 ( 32) SS BOND : angle 1.05189 ( 64) covalent geometry : bond 0.00289 (14580) covalent geometry : angle 0.64529 (19784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6396.19 seconds wall clock time: 112 minutes 16.72 seconds (6736.72 seconds total)