Starting phenix.real_space_refine on Fri Jun 5 06:34:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxa_64578/06_2026/9uxa_64578.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxa_64578/06_2026/9uxa_64578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uxa_64578/06_2026/9uxa_64578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxa_64578/06_2026/9uxa_64578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxa_64578/06_2026/9uxa_64578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxa_64578/06_2026/9uxa_64578.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 284 5.49 5 S 55 5.16 5 C 10761 2.51 5 N 3361 2.21 5 O 4032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2782 Classifications: {'peptide': 356} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 337} Chain breaks: 1 Chain: "J" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3112 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 21, 'TRANS': 378} Chain breaks: 2 Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 457 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain breaks: 1 Chain: "L" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 365 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Chain: "X" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2929 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "Y" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2892 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Time building chain proxies: 4.21, per 1000 atoms: 0.23 Number of scatterers: 18493 At special positions: 0 Unit cell: (100.44, 123.69, 175.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 284 15.00 O 4032 8.00 N 3361 7.00 C 10761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 670.5 milliseconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 20 sheets defined 55.6% alpha, 7.4% beta 104 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.735A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.546A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.820A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.600A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.529A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.590A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.610A pdb=" N ALA C 23 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 38 removed outlier: 3.736A pdb=" N VAL C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 75 removed outlier: 3.513A pdb=" N ILE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.576A pdb=" N LEU C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'D' and resid 35 through 46 removed outlier: 4.320A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.561A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.612A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.322A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.713A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.889A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.997A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.646A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.764A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 38 removed outlier: 3.667A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 42 removed outlier: 3.606A pdb=" N GLY F 42 " --> pdb=" O ARG F 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 39 through 42' Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE F 66 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.601A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.537A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 46 removed outlier: 3.875A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.644A pdb=" N VAL H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 removed outlier: 3.772A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG H 96 " --> pdb=" O GLN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 103 through 120 removed outlier: 3.563A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 92 removed outlier: 3.767A pdb=" N ILE I 85 " --> pdb=" O ASP I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.549A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 146 removed outlier: 3.552A pdb=" N GLY I 146 " --> pdb=" O LEU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 197 removed outlier: 3.636A pdb=" N ARG I 196 " --> pdb=" O ILE I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 222 through 227 removed outlier: 3.926A pdb=" N GLU I 226 " --> pdb=" O ASP I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 255 removed outlier: 3.536A pdb=" N ARG I 254 " --> pdb=" O GLY I 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE I 255 " --> pdb=" O ASN I 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 251 through 255' Processing helix chain 'I' and resid 256 through 257 No H-bonds generated for 'chain 'I' and resid 256 through 257' Processing helix chain 'I' and resid 258 through 263 removed outlier: 4.276A pdb=" N PHE I 262 " --> pdb=" O PRO I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 285 removed outlier: 3.629A pdb=" N CYS I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 289 through 296 removed outlier: 3.524A pdb=" N ASN I 296 " --> pdb=" O ASP I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 306 removed outlier: 3.606A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 303 through 306' Processing helix chain 'I' and resid 308 through 319 Processing helix chain 'I' and resid 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 337 through 348 Processing helix chain 'I' and resid 349 through 354 Processing helix chain 'I' and resid 358 through 366 Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'J' and resid 71 through 76 Processing helix chain 'J' and resid 95 through 110 removed outlier: 3.571A pdb=" N PHE J 99 " --> pdb=" O ASP J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 144 Processing helix chain 'J' and resid 154 through 162 removed outlier: 3.959A pdb=" N ASN J 162 " --> pdb=" O THR J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 192 removed outlier: 3.775A pdb=" N ILE J 192 " --> pdb=" O GLN J 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 189 through 192' Processing helix chain 'J' and resid 198 through 214 removed outlier: 3.577A pdb=" N GLN J 211 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU J 212 " --> pdb=" O GLU J 208 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET J 213 " --> pdb=" O LEU J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 266 Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 305 through 310 removed outlier: 3.979A pdb=" N PHE J 309 " --> pdb=" O PRO J 305 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 335 Processing helix chain 'J' and resid 340 through 346 Processing helix chain 'J' and resid 359 through 371 Processing helix chain 'J' and resid 391 through 402 removed outlier: 3.543A pdb=" N ILE J 395 " --> pdb=" O PHE J 391 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 417 Processing helix chain 'K' and resid 464 through 512 removed outlier: 3.746A pdb=" N ARG K 468 " --> pdb=" O GLN K 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 19 removed outlier: 3.527A pdb=" N VAL L 7 " --> pdb=" O SER L 3 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.150A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 44 through 45 removed outlier: 7.386A pdb=" N ARG C 44 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.054A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'I' and resid 29 through 32 removed outlier: 4.447A pdb=" N ALA I 29 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA I 19 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'I' and resid 150 through 152 removed outlier: 3.568A pdb=" N VAL I 152 " --> pdb=" O VAL I 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AB4, first strand: chain 'I' and resid 238 through 242 removed outlier: 3.519A pdb=" N LYS I 238 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN I 246 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 297 through 298 removed outlier: 6.917A pdb=" N THR I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'J' and resid 35 through 38 removed outlier: 3.889A pdb=" N VAL J 35 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA J 25 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE J 37 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER J 123 " --> pdb=" O PHE J 16 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE J 18 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS J 152 " --> pdb=" O MET J 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 68 through 69 Processing sheet with id=AB8, first strand: chain 'J' and resid 88 through 89 removed outlier: 3.636A pdb=" N LYS J 89 " --> pdb=" O MET J 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 186 through 187 removed outlier: 3.567A pdb=" N ALA J 179 " --> pdb=" O VAL J 193 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL J 193 " --> pdb=" O ALA J 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 186 through 187 removed outlier: 3.921A pdb=" N ILE J 169 " --> pdb=" O ILE J 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 31 through 37 removed outlier: 3.670A pdb=" N GLU L 32 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS L 47 " --> pdb=" O LYS L 34 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 274 hydrogen bonds 544 hydrogen bond angles 0 basepair planarities 104 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 2.46 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: 4862 1.34 - 1.46: 6048 1.46 - 1.58: 7850 1.58 - 1.71: 567 1.71 - 1.83: 94 Bond restraints: 19421 Sorted by residual: bond pdb=" N ILE B 46 " pdb=" CA ILE B 46 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.41e+00 bond pdb=" CB PRO I 102 " pdb=" CG PRO I 102 " ideal model delta sigma weight residual 1.492 1.634 -0.142 5.00e-02 4.00e+02 8.09e+00 bond pdb=" N ASN C 75 " pdb=" CA ASN C 75 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.26e-02 6.30e+03 8.04e+00 bond pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.47e+00 bond pdb=" P DC X 93 " pdb=" OP2 DC X 93 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.24e+00 ... (remaining 19416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 27236 3.19 - 6.37: 186 6.37 - 9.56: 32 9.56 - 12.75: 7 12.75 - 15.93: 3 Bond angle restraints: 27464 Sorted by residual: angle pdb=" C3' DC Y 26 " pdb=" O3' DC Y 26 " pdb=" P DT Y 27 " ideal model delta sigma weight residual 120.20 109.56 10.64 1.50e+00 4.44e-01 5.03e+01 angle pdb=" C3' DA X 3 " pdb=" O3' DA X 3 " pdb=" P DG X 4 " ideal model delta sigma weight residual 120.20 110.04 10.16 1.50e+00 4.44e-01 4.59e+01 angle pdb=" CA PRO I 102 " pdb=" N PRO I 102 " pdb=" CD PRO I 102 " ideal model delta sigma weight residual 112.00 103.01 8.99 1.40e+00 5.10e-01 4.12e+01 angle pdb=" CA MET I 190 " pdb=" CB MET I 190 " pdb=" CG MET I 190 " ideal model delta sigma weight residual 114.10 125.51 -11.41 2.00e+00 2.50e-01 3.26e+01 angle pdb=" N MET I 190 " pdb=" CA MET I 190 " pdb=" CB MET I 190 " ideal model delta sigma weight residual 110.41 119.39 -8.98 1.68e+00 3.54e-01 2.86e+01 ... (remaining 27459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 9434 35.85 - 71.71: 1480 71.71 - 107.56: 35 107.56 - 143.41: 1 143.41 - 179.27: 3 Dihedral angle restraints: 10953 sinusoidal: 6304 harmonic: 4649 Sorted by residual: dihedral pdb=" CA GLU I 226 " pdb=" C GLU I 226 " pdb=" N MET I 227 " pdb=" CA MET I 227 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA PHE J 297 " pdb=" C PHE J 297 " pdb=" N GLY J 298 " pdb=" CA GLY J 298 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CD ARG K1372 " pdb=" NE ARG K1372 " pdb=" CZ ARG K1372 " pdb=" NH1 ARG K1372 " ideal model delta sinusoidal sigma weight residual 0.00 -38.08 38.08 1 1.00e+01 1.00e-02 2.04e+01 ... (remaining 10950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3017 0.105 - 0.209: 75 0.209 - 0.314: 2 0.314 - 0.418: 0 0.418 - 0.523: 7 Chirality restraints: 3101 Sorted by residual: chirality pdb=" P DG X 95 " pdb=" OP1 DG X 95 " pdb=" OP2 DG X 95 " pdb=" O5' DG X 95 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" P DC X 93 " pdb=" OP1 DC X 93 " pdb=" OP2 DC X 93 " pdb=" O5' DC X 93 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.50 2.00e-01 2.50e+01 6.23e+00 chirality pdb=" P DC Y 26 " pdb=" OP1 DC Y 26 " pdb=" OP2 DC Y 26 " pdb=" O5' DC Y 26 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.49 2.00e-01 2.50e+01 6.10e+00 ... (remaining 3098 not shown) Planarity restraints: 2509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K1372 " -0.668 9.50e-02 1.11e+02 2.99e-01 5.46e+01 pdb=" NE ARG K1372 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG K1372 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG K1372 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K1372 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE J 180 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO J 181 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO J 181 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO J 181 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 29 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C ARG L 29 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG L 29 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS L 30 " 0.019 2.00e-02 2.50e+03 ... (remaining 2506 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 211 2.61 - 3.19: 14317 3.19 - 3.76: 32462 3.76 - 4.33: 42100 4.33 - 4.90: 62927 Nonbonded interactions: 152017 Sorted by model distance: nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR I 202 " pdb=" OE1 GLU I 205 " model vdw 2.210 3.040 nonbonded pdb=" O GLY J 199 " pdb=" OG1 THR J 203 " model vdw 2.264 3.040 nonbonded pdb=" O VAL L 7 " pdb=" OG1 THR L 11 " model vdw 2.294 3.040 nonbonded pdb=" OD2 ASP J 17 " pdb=" OG SER J 393 " model vdw 2.297 3.040 ... (remaining 152012 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' and resid 39 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and (resid 17 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 120)) selection = (chain 'G' and (resid 15 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 122)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 19421 Z= 0.195 Angle : 0.776 15.933 27464 Z= 0.426 Chirality : 0.047 0.523 3101 Planarity : 0.009 0.299 2509 Dihedral : 25.605 179.266 7955 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 0.37 % Allowed : 29.62 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1572 helix: -0.94 (0.17), residues: 802 sheet: -0.59 (0.51), residues: 96 loop : -1.26 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 44 TYR 0.028 0.001 TYR J 293 PHE 0.046 0.002 PHE J 210 TRP 0.041 0.002 TRP J 394 HIS 0.010 0.001 HIS K 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (19421) covalent geometry : angle 0.77602 / 0.43 (27464) hydrogen bonds : bond 0.21470 / 14.06 ( 875) hydrogen bonds : angle 6.92421 / 4.85 ( 2290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 427 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 THR cc_start: 0.8581 (t) cc_final: 0.8357 (p) REVERT: C 40 ASN cc_start: 0.6769 (m-40) cc_final: 0.6531 (m-40) REVERT: C 75 ASN cc_start: 0.7822 (t0) cc_final: 0.7456 (t0) REVERT: D 32 GLU cc_start: 0.7918 (pp20) cc_final: 0.7433 (pp20) REVERT: E 58 THR cc_start: 0.8127 (p) cc_final: 0.7835 (p) REVERT: E 64 LYS cc_start: 0.8435 (mptt) cc_final: 0.8198 (mptt) REVERT: E 94 GLU cc_start: 0.7940 (tp30) cc_final: 0.7601 (mm-30) REVERT: F 84 MET cc_start: 0.8097 (mmm) cc_final: 0.7767 (tpt) REVERT: F 87 VAL cc_start: 0.8839 (p) cc_final: 0.8624 (m) REVERT: H 39 TYR cc_start: 0.7602 (t80) cc_final: 0.7392 (t80) REVERT: H 59 MET cc_start: 0.9103 (mmm) cc_final: 0.8882 (mmp) REVERT: I 122 ILE cc_start: 0.7480 (mt) cc_final: 0.7092 (mt) REVERT: I 143 TYR cc_start: 0.7942 (m-80) cc_final: 0.7726 (m-80) REVERT: I 152 VAL cc_start: 0.7769 (p) cc_final: 0.7418 (t) REVERT: I 221 LEU cc_start: 0.7640 (mm) cc_final: 0.7252 (tt) REVERT: I 257 CYS cc_start: 0.8360 (t) cc_final: 0.8069 (t) REVERT: I 292 ASP cc_start: 0.7903 (m-30) cc_final: 0.7547 (t0) REVERT: I 296 ASN cc_start: 0.6427 (m110) cc_final: 0.5329 (m110) REVERT: J 43 MET cc_start: 0.6836 (tmm) cc_final: 0.6545 (tmm) REVERT: J 107 TYR cc_start: 0.7890 (m-80) cc_final: 0.7633 (m-80) REVERT: J 119 PRO cc_start: 0.8322 (Cg_exo) cc_final: 0.8016 (Cg_endo) REVERT: J 158 THR cc_start: 0.7739 (m) cc_final: 0.7100 (p) REVERT: J 175 THR cc_start: 0.7939 (p) cc_final: 0.7393 (p) REVERT: J 265 SER cc_start: 0.8258 (m) cc_final: 0.7842 (p) REVERT: J 322 MET cc_start: 0.6881 (tpp) cc_final: 0.6678 (tpp) REVERT: K 472 HIS cc_start: 0.7174 (t70) cc_final: 0.6740 (t70) REVERT: K 504 VAL cc_start: 0.7445 (m) cc_final: 0.7099 (t) outliers start: 5 outliers final: 3 residues processed: 430 average time/residue: 0.1763 time to fit residues: 107.6525 Evaluate side-chains 285 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 282 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 318 THR Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain J residue 357 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0020 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS H 79 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 HIS J 205 GLN J 251 HIS J 260 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.121623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093381 restraints weight = 41359.386| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.61 r_work: 0.3317 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19421 Z= 0.228 Angle : 0.688 10.411 27464 Z= 0.379 Chirality : 0.041 0.264 3101 Planarity : 0.006 0.080 2509 Dihedral : 27.972 176.989 4863 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 4.73 % Allowed : 25.04 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.20), residues: 1572 helix: -0.33 (0.18), residues: 839 sheet: -0.53 (0.46), residues: 111 loop : -1.23 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 468 TYR 0.030 0.002 TYR B 98 PHE 0.022 0.002 PHE J 210 TRP 0.017 0.002 TRP J 394 HIS 0.008 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (19421) covalent geometry : angle 0.68818 / 0.38 (27464) hydrogen bonds : bond 0.04815 / 3.32 ( 875) hydrogen bonds : angle 4.17694 / 2.96 ( 2290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 298 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8707 (ptm-80) cc_final: 0.8470 (ptm-80) REVERT: C 40 ASN cc_start: 0.7863 (m-40) cc_final: 0.7416 (m-40) REVERT: D 32 GLU cc_start: 0.7740 (pp20) cc_final: 0.7199 (pp20) REVERT: E 48 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8876 (mp) REVERT: E 58 THR cc_start: 0.8763 (p) cc_final: 0.8460 (p) REVERT: E 105 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7919 (mt-10) REVERT: E 112 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9126 (mp) REVERT: H 57 SER cc_start: 0.8650 (t) cc_final: 0.8422 (m) REVERT: H 90 GLU cc_start: 0.8311 (mp0) cc_final: 0.8090 (mp0) REVERT: I 101 HIS cc_start: 0.8013 (m-70) cc_final: 0.7442 (m-70) REVERT: I 122 ILE cc_start: 0.7562 (mt) cc_final: 0.7243 (mt) REVERT: I 153 MET cc_start: 0.7245 (tmm) cc_final: 0.7045 (tmm) REVERT: I 207 GLU cc_start: 0.8250 (tt0) cc_final: 0.7904 (tm-30) REVERT: I 221 LEU cc_start: 0.8203 (mm) cc_final: 0.7641 (tt) REVERT: I 227 MET cc_start: 0.7477 (mtm) cc_final: 0.7111 (mtm) REVERT: I 257 CYS cc_start: 0.8632 (t) cc_final: 0.8389 (t) REVERT: I 292 ASP cc_start: 0.8509 (m-30) cc_final: 0.7946 (t0) REVERT: I 355 MET cc_start: 0.6096 (ptt) cc_final: 0.5887 (ptt) REVERT: J 89 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8551 (pmtt) REVERT: J 104 ASP cc_start: 0.8493 (p0) cc_final: 0.8256 (t0) REVERT: J 222 MET cc_start: 0.6342 (mtt) cc_final: 0.5946 (mtt) REVERT: J 227 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6293 (pp20) REVERT: J 265 SER cc_start: 0.8468 (m) cc_final: 0.7964 (p) REVERT: J 391 PHE cc_start: 0.7541 (m-10) cc_final: 0.7316 (m-10) REVERT: J 403 LEU cc_start: 0.8896 (mt) cc_final: 0.8643 (tp) REVERT: J 409 MET cc_start: 0.7939 (pmm) cc_final: 0.7714 (pmm) REVERT: J 410 TRP cc_start: 0.8520 (m100) cc_final: 0.8073 (m100) REVERT: K 472 HIS cc_start: 0.7789 (t70) cc_final: 0.7376 (t70) outliers start: 64 outliers final: 29 residues processed: 343 average time/residue: 0.1510 time to fit residues: 76.1767 Evaluate side-chains 287 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 263 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 76 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.119687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091203 restraints weight = 41474.541| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.59 r_work: 0.3277 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19421 Z= 0.184 Angle : 0.609 10.815 27464 Z= 0.338 Chirality : 0.038 0.148 3101 Planarity : 0.005 0.059 2509 Dihedral : 28.005 179.836 4859 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 95.99 % Rotamer: Outliers : 4.87 % Allowed : 24.30 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1572 helix: 0.39 (0.18), residues: 837 sheet: -0.19 (0.45), residues: 115 loop : -1.15 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 466 TYR 0.021 0.002 TYR B 98 PHE 0.018 0.002 PHE J 210 TRP 0.015 0.001 TRP J 394 HIS 0.010 0.001 HIS I 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (19421) covalent geometry : angle 0.60923 / 0.34 (27464) hydrogen bonds : bond 0.04096 / 2.83 ( 875) hydrogen bonds : angle 3.83179 / 2.72 ( 2290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 271 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8033 (m-40) cc_final: 0.7785 (m-40) REVERT: C 95 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8951 (mt) REVERT: E 58 THR cc_start: 0.8897 (p) cc_final: 0.8646 (p) REVERT: E 94 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 108 ASN cc_start: 0.8864 (t0) cc_final: 0.8400 (t0) REVERT: E 112 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9108 (mp) REVERT: H 57 SER cc_start: 0.8824 (t) cc_final: 0.8515 (m) REVERT: H 90 GLU cc_start: 0.8381 (mp0) cc_final: 0.8118 (mp0) REVERT: I 8 LEU cc_start: 0.8089 (mm) cc_final: 0.7866 (mp) REVERT: I 101 HIS cc_start: 0.8229 (m-70) cc_final: 0.7688 (m-70) REVERT: I 122 ILE cc_start: 0.7512 (mt) cc_final: 0.7179 (mt) REVERT: I 152 VAL cc_start: 0.8662 (p) cc_final: 0.8371 (t) REVERT: I 161 HIS cc_start: 0.7665 (m-70) cc_final: 0.7001 (m170) REVERT: I 207 GLU cc_start: 0.8258 (tt0) cc_final: 0.7965 (tm-30) REVERT: I 221 LEU cc_start: 0.8217 (mm) cc_final: 0.7775 (tt) REVERT: I 227 MET cc_start: 0.7608 (mtm) cc_final: 0.7354 (mtm) REVERT: I 248 ILE cc_start: 0.8049 (mp) cc_final: 0.7806 (mm) REVERT: I 257 CYS cc_start: 0.8709 (t) cc_final: 0.8468 (t) REVERT: I 292 ASP cc_start: 0.8525 (m-30) cc_final: 0.8001 (t0) REVERT: J 32 CYS cc_start: 0.6312 (OUTLIER) cc_final: 0.5877 (t) REVERT: J 89 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8493 (pmtt) REVERT: J 265 SER cc_start: 0.8553 (m) cc_final: 0.8285 (p) REVERT: J 403 LEU cc_start: 0.8934 (mt) cc_final: 0.8709 (tp) REVERT: J 410 TRP cc_start: 0.8617 (m100) cc_final: 0.8345 (m100) REVERT: K 506 THR cc_start: 0.8194 (t) cc_final: 0.7836 (p) outliers start: 66 outliers final: 41 residues processed: 316 average time/residue: 0.1540 time to fit residues: 72.4067 Evaluate side-chains 297 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 252 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain J residue 296 ASP Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 349 ILE Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain L residue 45 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.119540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091212 restraints weight = 41396.353| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.58 r_work: 0.3275 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19421 Z= 0.151 Angle : 0.582 9.688 27464 Z= 0.324 Chirality : 0.037 0.141 3101 Planarity : 0.004 0.057 2509 Dihedral : 27.891 179.828 4859 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 3.99 % Allowed : 25.11 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.21), residues: 1572 helix: 0.83 (0.19), residues: 835 sheet: -0.24 (0.46), residues: 109 loop : -1.02 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 466 TYR 0.016 0.001 TYR B 98 PHE 0.014 0.001 PHE J 210 TRP 0.012 0.001 TRP J 394 HIS 0.009 0.001 HIS K 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (19421) covalent geometry : angle 0.58215 / 0.32 (27464) hydrogen bonds : bond 0.03563 / 2.47 ( 875) hydrogen bonds : angle 3.67964 / 2.61 ( 2290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 261 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8035 (m-40) cc_final: 0.7782 (m-40) REVERT: C 95 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8957 (mt) REVERT: D 59 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (mmt) REVERT: E 58 THR cc_start: 0.8906 (p) cc_final: 0.8659 (p) REVERT: E 94 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 108 ASN cc_start: 0.8845 (t0) cc_final: 0.8482 (t0) REVERT: E 112 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9087 (mp) REVERT: H 57 SER cc_start: 0.8819 (t) cc_final: 0.8493 (m) REVERT: H 90 GLU cc_start: 0.8319 (mp0) cc_final: 0.8063 (mp0) REVERT: I 8 LEU cc_start: 0.8050 (mm) cc_final: 0.7813 (mp) REVERT: I 122 ILE cc_start: 0.7454 (mt) cc_final: 0.7110 (mt) REVERT: I 161 HIS cc_start: 0.7643 (m-70) cc_final: 0.6934 (m170) REVERT: I 190 MET cc_start: 0.8670 (pmm) cc_final: 0.8469 (pmm) REVERT: I 207 GLU cc_start: 0.8243 (tt0) cc_final: 0.7995 (tm-30) REVERT: I 221 LEU cc_start: 0.8176 (mm) cc_final: 0.7808 (tt) REVERT: I 227 MET cc_start: 0.7499 (mtm) cc_final: 0.7105 (mtm) REVERT: I 248 ILE cc_start: 0.8046 (mp) cc_final: 0.7812 (mm) REVERT: I 257 CYS cc_start: 0.8621 (t) cc_final: 0.8403 (t) REVERT: I 292 ASP cc_start: 0.8509 (m-30) cc_final: 0.8127 (t0) REVERT: I 296 ASN cc_start: 0.7670 (m110) cc_final: 0.7267 (m-40) REVERT: J 32 CYS cc_start: 0.6357 (OUTLIER) cc_final: 0.5936 (t) REVERT: J 89 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8421 (pmtt) REVERT: J 265 SER cc_start: 0.8585 (m) cc_final: 0.8354 (p) REVERT: J 376 MET cc_start: 0.7741 (pmm) cc_final: 0.7448 (pmm) REVERT: J 410 TRP cc_start: 0.8626 (m100) cc_final: 0.8184 (m100) REVERT: K 466 ARG cc_start: 0.8102 (mmt-90) cc_final: 0.7843 (mpt180) REVERT: L 34 LYS cc_start: 0.7880 (pttt) cc_final: 0.7507 (pttm) outliers start: 54 outliers final: 34 residues processed: 300 average time/residue: 0.1522 time to fit residues: 68.1383 Evaluate side-chains 283 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 349 ILE Chi-restraints excluded: chain L residue 45 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 GLN K 472 HIS ** K 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.115050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087291 restraints weight = 41042.960| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.57 r_work: 0.3177 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19421 Z= 0.239 Angle : 0.651 12.346 27464 Z= 0.357 Chirality : 0.040 0.153 3101 Planarity : 0.005 0.057 2509 Dihedral : 28.292 179.153 4859 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 5.69 % Allowed : 24.30 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1572 helix: 0.91 (0.18), residues: 848 sheet: -0.04 (0.47), residues: 121 loop : -1.08 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 89 TYR 0.020 0.002 TYR B 98 PHE 0.020 0.002 PHE I 279 TRP 0.020 0.002 TRP J 394 HIS 0.008 0.001 HIS K 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 (19421) covalent geometry : angle 0.65084 / 0.36 (27464) hydrogen bonds : bond 0.04496 / 3.18 ( 875) hydrogen bonds : angle 3.68883 / 2.62 ( 2290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 250 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8796 (p) cc_final: 0.8546 (p) REVERT: B 80 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8792 (p) REVERT: C 95 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.8860 (mt) REVERT: D 59 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8321 (mmt) REVERT: E 48 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9034 (mp) REVERT: E 94 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8202 (mm-30) REVERT: E 108 ASN cc_start: 0.8930 (t0) cc_final: 0.8512 (t0) REVERT: E 112 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9126 (mp) REVERT: H 57 SER cc_start: 0.8927 (t) cc_final: 0.8505 (m) REVERT: H 90 GLU cc_start: 0.8407 (mp0) cc_final: 0.8086 (mp0) REVERT: I 122 ILE cc_start: 0.7669 (mt) cc_final: 0.7316 (mt) REVERT: I 162 THR cc_start: 0.7770 (p) cc_final: 0.7426 (p) REVERT: I 177 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7213 (ptm-80) REVERT: I 207 GLU cc_start: 0.8293 (tt0) cc_final: 0.8023 (tm-30) REVERT: I 221 LEU cc_start: 0.8280 (mm) cc_final: 0.7878 (tt) REVERT: I 227 MET cc_start: 0.7509 (mtm) cc_final: 0.7188 (mtm) REVERT: I 248 ILE cc_start: 0.7911 (mp) cc_final: 0.7699 (mm) REVERT: I 257 CYS cc_start: 0.8793 (t) cc_final: 0.8591 (t) REVERT: I 283 MET cc_start: 0.8660 (ptm) cc_final: 0.8377 (ptt) REVERT: I 292 ASP cc_start: 0.8689 (m-30) cc_final: 0.8267 (t0) REVERT: I 296 ASN cc_start: 0.8093 (m110) cc_final: 0.7759 (m-40) REVERT: J 89 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8322 (pmtt) REVERT: J 227 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6550 (pp20) REVERT: J 265 SER cc_start: 0.8724 (m) cc_final: 0.8521 (p) REVERT: J 410 TRP cc_start: 0.8841 (m100) cc_final: 0.8390 (m100) REVERT: K 466 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7731 (mpt180) REVERT: L 34 LYS cc_start: 0.7922 (pttt) cc_final: 0.7487 (pttm) outliers start: 77 outliers final: 40 residues processed: 308 average time/residue: 0.1487 time to fit residues: 68.6739 Evaluate side-chains 285 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 237 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 345 TYR Chi-restraints excluded: chain J residue 349 ILE Chi-restraints excluded: chain L residue 45 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 36 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 46 HIS ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 HIS ** K 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.117852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089292 restraints weight = 41028.857| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.56 r_work: 0.3242 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19421 Z= 0.147 Angle : 0.602 9.146 27464 Z= 0.331 Chirality : 0.037 0.197 3101 Planarity : 0.004 0.057 2509 Dihedral : 27.925 179.156 4859 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 4.06 % Allowed : 25.33 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.22), residues: 1572 helix: 1.29 (0.18), residues: 843 sheet: -0.08 (0.46), residues: 121 loop : -0.94 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 79 TYR 0.014 0.001 TYR K 475 PHE 0.012 0.001 PHE J 210 TRP 0.034 0.001 TRP J 394 HIS 0.006 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (19421) covalent geometry : angle 0.60203 / 0.33 (27464) hydrogen bonds : bond 0.03477 / 2.40 ( 875) hydrogen bonds : angle 3.59494 / 2.53 ( 2290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8870 (mt) REVERT: C 101 ARG cc_start: 0.7807 (mtp180) cc_final: 0.7234 (mmm160) REVERT: D 59 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8316 (mmt) REVERT: E 94 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8188 (mm-30) REVERT: E 108 ASN cc_start: 0.8833 (t0) cc_final: 0.8393 (t0) REVERT: E 112 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9122 (mp) REVERT: H 57 SER cc_start: 0.8946 (t) cc_final: 0.8523 (m) REVERT: H 90 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: I 122 ILE cc_start: 0.7542 (mt) cc_final: 0.7181 (mt) REVERT: I 162 THR cc_start: 0.7813 (p) cc_final: 0.7500 (p) REVERT: I 207 GLU cc_start: 0.8286 (tt0) cc_final: 0.8041 (tm-30) REVERT: I 221 LEU cc_start: 0.8361 (mm) cc_final: 0.7903 (tt) REVERT: I 227 MET cc_start: 0.7562 (mtm) cc_final: 0.7314 (mtm) REVERT: I 257 CYS cc_start: 0.8806 (t) cc_final: 0.8605 (t) REVERT: I 283 MET cc_start: 0.8716 (ptm) cc_final: 0.8500 (ptt) REVERT: I 292 ASP cc_start: 0.8754 (m-30) cc_final: 0.8272 (t0) REVERT: I 296 ASN cc_start: 0.8134 (m110) cc_final: 0.7810 (m-40) REVERT: I 369 ILE cc_start: 0.8225 (tp) cc_final: 0.7966 (mm) REVERT: J 227 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6622 (pp20) REVERT: J 265 SER cc_start: 0.8758 (m) cc_final: 0.8529 (p) REVERT: J 322 MET cc_start: 0.7667 (tpp) cc_final: 0.7339 (tpp) REVERT: J 410 TRP cc_start: 0.8755 (m100) cc_final: 0.8299 (m100) REVERT: L 29 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7853 (ttp80) REVERT: L 34 LYS cc_start: 0.7899 (pttt) cc_final: 0.7585 (pttm) outliers start: 55 outliers final: 34 residues processed: 283 average time/residue: 0.1462 time to fit residues: 62.0510 Evaluate side-chains 270 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain J residue 45 VAL Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 345 TYR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 45 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 160 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 46 HIS ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.115805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088082 restraints weight = 41121.370| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.58 r_work: 0.3197 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19421 Z= 0.199 Angle : 0.634 12.247 27464 Z= 0.346 Chirality : 0.039 0.196 3101 Planarity : 0.005 0.056 2509 Dihedral : 28.061 179.675 4859 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.36 % Rotamer: Outliers : 4.21 % Allowed : 25.11 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1572 helix: 1.27 (0.18), residues: 855 sheet: 0.17 (0.49), residues: 110 loop : -0.89 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.026 0.002 TYR F 88 PHE 0.011 0.001 PHE I 262 TRP 0.035 0.001 TRP J 394 HIS 0.007 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (19421) covalent geometry : angle 0.63441 / 0.35 (27464) hydrogen bonds : bond 0.03964 / 2.79 ( 875) hydrogen bonds : angle 3.62522 / 2.55 ( 2290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8780 (p) REVERT: C 95 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8862 (mt) REVERT: C 101 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7299 (mmm160) REVERT: D 59 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8326 (mmt) REVERT: E 108 ASN cc_start: 0.8892 (t0) cc_final: 0.8438 (t0) REVERT: E 112 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9126 (mp) REVERT: F 63 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7930 (mt-10) REVERT: H 57 SER cc_start: 0.8962 (t) cc_final: 0.8508 (m) REVERT: H 90 GLU cc_start: 0.8488 (mp0) cc_final: 0.8165 (mp0) REVERT: I 122 ILE cc_start: 0.7663 (mt) cc_final: 0.7315 (mt) REVERT: I 162 THR cc_start: 0.7855 (p) cc_final: 0.7549 (p) REVERT: I 207 GLU cc_start: 0.8289 (tt0) cc_final: 0.8015 (tm-30) REVERT: I 221 LEU cc_start: 0.8322 (mm) cc_final: 0.7866 (tt) REVERT: I 227 MET cc_start: 0.7551 (mtm) cc_final: 0.7334 (mtm) REVERT: I 248 ILE cc_start: 0.7635 (mm) cc_final: 0.7319 (tp) REVERT: I 292 ASP cc_start: 0.8871 (m-30) cc_final: 0.8357 (t0) REVERT: J 195 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8532 (m) REVERT: J 227 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6643 (pp20) REVERT: J 265 SER cc_start: 0.8747 (m) cc_final: 0.8529 (p) REVERT: J 322 MET cc_start: 0.7788 (tpp) cc_final: 0.7533 (tpp) REVERT: L 34 LYS cc_start: 0.7896 (pttt) cc_final: 0.7653 (pttm) outliers start: 57 outliers final: 41 residues processed: 273 average time/residue: 0.1463 time to fit residues: 60.0206 Evaluate side-chains 271 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 274 TYR Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 345 TYR Chi-restraints excluded: chain J residue 349 ILE Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 45 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 138 optimal weight: 0.0870 chunk 38 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 46 HIS ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.117368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089955 restraints weight = 41008.646| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.62 r_work: 0.3234 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19421 Z= 0.145 Angle : 0.614 12.087 27464 Z= 0.333 Chirality : 0.037 0.288 3101 Planarity : 0.004 0.056 2509 Dihedral : 27.872 179.372 4859 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 3.99 % Allowed : 25.70 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1572 helix: 1.44 (0.18), residues: 862 sheet: 0.17 (0.48), residues: 110 loop : -0.83 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.027 0.001 TYR F 88 PHE 0.011 0.001 PHE J 210 TRP 0.030 0.001 TRP J 394 HIS 0.007 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (19421) covalent geometry : angle 0.61447 / 0.33 (27464) hydrogen bonds : bond 0.03421 / 2.36 ( 875) hydrogen bonds : angle 3.56051 / 2.50 ( 2290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8855 (mt) REVERT: D 59 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8340 (mmt) REVERT: E 94 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8128 (mm-30) REVERT: E 108 ASN cc_start: 0.8826 (t0) cc_final: 0.8366 (t0) REVERT: E 112 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9119 (mp) REVERT: H 57 SER cc_start: 0.8948 (t) cc_final: 0.8533 (m) REVERT: H 90 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: I 122 ILE cc_start: 0.7560 (mt) cc_final: 0.7200 (mt) REVERT: I 161 HIS cc_start: 0.7743 (m90) cc_final: 0.7540 (m90) REVERT: I 162 THR cc_start: 0.7873 (p) cc_final: 0.7584 (p) REVERT: I 207 GLU cc_start: 0.8264 (tt0) cc_final: 0.8026 (tm-30) REVERT: I 221 LEU cc_start: 0.8328 (mm) cc_final: 0.7923 (tt) REVERT: I 248 ILE cc_start: 0.7708 (mm) cc_final: 0.7375 (tp) REVERT: I 292 ASP cc_start: 0.8888 (m-30) cc_final: 0.8325 (t0) REVERT: J 122 MET cc_start: 0.8411 (ttt) cc_final: 0.8167 (mtp) REVERT: J 195 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8480 (m) REVERT: J 227 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6642 (pp20) REVERT: J 322 MET cc_start: 0.7811 (tpp) cc_final: 0.7328 (tpp) REVERT: L 32 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5779 (mm-30) REVERT: L 34 LYS cc_start: 0.7948 (pttt) cc_final: 0.7712 (pttm) outliers start: 54 outliers final: 39 residues processed: 278 average time/residue: 0.1439 time to fit residues: 60.2131 Evaluate side-chains 275 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 274 TYR Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain J residue 345 TYR Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 45 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 69 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 85 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 167 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.116308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088656 restraints weight = 41070.741| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.60 r_work: 0.3204 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19421 Z= 0.178 Angle : 0.632 12.717 27464 Z= 0.341 Chirality : 0.038 0.287 3101 Planarity : 0.004 0.057 2509 Dihedral : 27.958 179.296 4859 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 4.21 % Allowed : 25.70 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1572 helix: 1.49 (0.18), residues: 863 sheet: 0.11 (0.48), residues: 110 loop : -0.86 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 62 TYR 0.023 0.002 TYR F 88 PHE 0.011 0.001 PHE J 210 TRP 0.033 0.002 TRP J 394 HIS 0.005 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (19421) covalent geometry : angle 0.63182 / 0.34 (27464) hydrogen bonds : bond 0.03701 / 2.58 ( 875) hydrogen bonds : angle 3.56605 / 2.51 ( 2290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8856 (mt) REVERT: C 99 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 101 ARG cc_start: 0.8272 (mmt180) cc_final: 0.8066 (mmt180) REVERT: D 59 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8324 (mmt) REVERT: E 94 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8172 (mm-30) REVERT: E 108 ASN cc_start: 0.8862 (t0) cc_final: 0.8391 (t0) REVERT: E 112 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.9127 (mp) REVERT: F 93 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7352 (mm-40) REVERT: H 57 SER cc_start: 0.8964 (t) cc_final: 0.8536 (m) REVERT: H 90 GLU cc_start: 0.8494 (mp0) cc_final: 0.8179 (mp0) REVERT: I 122 ILE cc_start: 0.7466 (mt) cc_final: 0.7124 (mt) REVERT: I 162 THR cc_start: 0.7906 (p) cc_final: 0.7611 (p) REVERT: I 190 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8712 (pmm) REVERT: I 207 GLU cc_start: 0.8303 (tt0) cc_final: 0.8067 (tm-30) REVERT: I 221 LEU cc_start: 0.8435 (mm) cc_final: 0.8068 (tt) REVERT: I 248 ILE cc_start: 0.7763 (mm) cc_final: 0.7425 (tp) REVERT: I 292 ASP cc_start: 0.8902 (m-30) cc_final: 0.8389 (t0) REVERT: J 195 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8591 (m) REVERT: J 227 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6696 (pp20) REVERT: K 468 ARG cc_start: 0.7000 (tpt90) cc_final: 0.6462 (tpt90) REVERT: L 32 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5845 (mm-30) REVERT: L 34 LYS cc_start: 0.7962 (pttt) cc_final: 0.7721 (pttm) outliers start: 57 outliers final: 42 residues processed: 273 average time/residue: 0.1469 time to fit residues: 60.1651 Evaluate side-chains 276 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 274 TYR Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 45 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 111 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.117772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089764 restraints weight = 41148.903| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.66 r_work: 0.3228 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19421 Z= 0.144 Angle : 0.628 12.564 27464 Z= 0.337 Chirality : 0.037 0.338 3101 Planarity : 0.004 0.057 2509 Dihedral : 27.754 179.235 4859 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 3.40 % Allowed : 26.37 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.22), residues: 1572 helix: 1.64 (0.18), residues: 862 sheet: 0.02 (0.48), residues: 110 loop : -0.78 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 62 TYR 0.020 0.001 TYR F 88 PHE 0.010 0.001 PHE J 210 TRP 0.037 0.002 TRP J 394 HIS 0.005 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (19421) covalent geometry : angle 0.62776 / 0.34 (27464) hydrogen bonds : bond 0.03341 / 2.28 ( 875) hydrogen bonds : angle 3.53603 / 2.49 ( 2290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8848 (mt) REVERT: C 99 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8612 (mt) REVERT: D 59 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8279 (mmt) REVERT: E 108 ASN cc_start: 0.8822 (t0) cc_final: 0.8358 (t0) REVERT: E 112 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9127 (mp) REVERT: F 93 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7323 (mm-40) REVERT: H 57 SER cc_start: 0.8995 (t) cc_final: 0.8557 (m) REVERT: H 90 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8225 (mp0) REVERT: I 122 ILE cc_start: 0.7424 (mt) cc_final: 0.7102 (mt) REVERT: I 162 THR cc_start: 0.7924 (p) cc_final: 0.7608 (p) REVERT: I 207 GLU cc_start: 0.8372 (tt0) cc_final: 0.8081 (tm-30) REVERT: I 221 LEU cc_start: 0.8499 (mm) cc_final: 0.8073 (tt) REVERT: I 248 ILE cc_start: 0.7781 (mm) cc_final: 0.7448 (tp) REVERT: I 292 ASP cc_start: 0.8946 (m-30) cc_final: 0.8427 (t0) REVERT: I 296 ASN cc_start: 0.8386 (m-40) cc_final: 0.8060 (m-40) REVERT: J 92 MET cc_start: 0.8436 (mmm) cc_final: 0.8100 (mmt) REVERT: J 195 SER cc_start: 0.9230 (OUTLIER) cc_final: 0.8595 (m) REVERT: J 227 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6698 (pp20) REVERT: K 468 ARG cc_start: 0.7023 (tpt90) cc_final: 0.6486 (tpt90) REVERT: L 32 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5833 (mm-30) REVERT: L 34 LYS cc_start: 0.7904 (pttt) cc_final: 0.7680 (pttm) outliers start: 46 outliers final: 33 residues processed: 267 average time/residue: 0.1459 time to fit residues: 58.5324 Evaluate side-chains 273 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 82 MET Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 132 MET Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 190 MET Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 211 ASP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 355 MET Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 195 SER Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 336 CYS Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 45 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.116498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089193 restraints weight = 41094.698| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.58 r_work: 0.3214 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19421 Z= 0.175 Angle : 0.644 12.379 27464 Z= 0.345 Chirality : 0.038 0.348 3101 Planarity : 0.004 0.056 2509 Dihedral : 27.891 179.143 4859 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 3.55 % Allowed : 26.44 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.22), residues: 1572 helix: 1.61 (0.18), residues: 865 sheet: -0.25 (0.47), residues: 116 loop : -0.75 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 62 TYR 0.022 0.002 TYR H 80 PHE 0.011 0.001 PHE J 210 TRP 0.039 0.002 TRP J 394 HIS 0.004 0.001 HIS J 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (19421) covalent geometry : angle 0.64396 / 0.35 (27464) hydrogen bonds : bond 0.03661 / 2.55 ( 875) hydrogen bonds : angle 3.56256 / 2.51 ( 2290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5586.30 seconds wall clock time: 95 minutes 53.47 seconds (5753.47 seconds total)