Starting phenix.real_space_refine on Sat Jul 4 05:41:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxa_64578/07_2026/9uxa_64578.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxa_64578/07_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_64578/07_2026/9uxa_64578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxa_64578/07_2026/9uxa_64578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uxa_64578/07_2026/9uxa_64578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxa_64578/07_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-6108/lib/python3.11/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: 3.84, per 1000 atoms: 0.21 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: 1.61 Conformation dependent library (CDL) restraints added in 572.1 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: 2.30 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: 3.86 Time building geometry restraints manager: 2.16 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=" C1' DT Y 35 " pdb=" N1 DT Y 35 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" C3' DT Y 138 " pdb=" C2' DT Y 138 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.55e+01 bond pdb=" C3' DG Y 33 " pdb=" C2' DG Y 33 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DG Y 146 " pdb=" C2' DG Y 146 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.65e+00 bond pdb=" C5' DA Y 39 " pdb=" C4' DA Y 39 " ideal model delta sigma weight residual 1.512 1.534 -0.022 7.00e-03 2.04e+04 9.54e+00 ... (remaining 19416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 27228 3.19 - 6.37: 194 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 - 0.107: 3009 0.107 - 0.213: 83 0.213 - 0.320: 2 0.320 - 0.426: 0 0.426 - 0.533: 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 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.10e+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 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.48e+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 2.34 -2.84 -0.50 2.00e-01 2.50e+01 6.35e+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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.090 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 19421 Z= 0.476 Angle : 0.867 15.933 27464 Z= 0.661 Chirality : 0.053 0.533 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 0.00550 / 0.48 (19421) covalent geometry : angle 0.86685 / 0.66 (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 : 0.697 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: 0.1707 time to fit residues: 105.0735 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 : 0.547 ------------------------------------------------------------------------------- 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... 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 H 79 HIS ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 GLN J 251 HIS J 260 GLN J 422 GLN ** K 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.124907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.096686 restraints weight = 41397.067| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.68 r_work: 0.3382 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 19421 Z= 0.214 Angle : 0.716 8.449 27464 Z= 0.397 Chirality : 0.045 0.252 3101 Planarity : 0.006 0.065 2509 Dihedral : 28.270 178.935 4863 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 4.51 % Allowed : 26.07 % Favored : 69.42 % 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: -1.15 (0.20), residues: 1572 helix: -0.30 (0.18), residues: 834 sheet: -0.95 (0.46), residues: 99 loop : -1.22 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 95 TYR 0.021 0.002 TYR G 57 PHE 0.018 0.003 PHE J 210 TRP 0.021 0.002 TRP L 48 HIS 0.008 0.002 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (19421) covalent geometry : angle 0.71564 / 0.40 (27464) hydrogen bonds : bond 0.05488 / 3.74 ( 875) hydrogen bonds : angle 4.40484 / 3.12 ( 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 351 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 290 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.7479 (m-40) cc_final: 0.7049 (m-40) REVERT: D 32 GLU cc_start: 0.7682 (pp20) cc_final: 0.7267 (pp20) REVERT: D 64 ASN cc_start: 0.9024 (m-40) cc_final: 0.8824 (m-40) REVERT: D 68 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8368 (mm-30) REVERT: E 48 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8839 (mp) REVERT: E 58 THR cc_start: 0.8623 (p) cc_final: 0.8328 (p) REVERT: E 105 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7870 (mt-10) REVERT: G 39 TYR cc_start: 0.8025 (m-10) cc_final: 0.7555 (m-10) REVERT: H 90 GLU cc_start: 0.8373 (mp0) cc_final: 0.8146 (mp0) REVERT: I 101 HIS cc_start: 0.8050 (m-70) cc_final: 0.7463 (m-70) REVERT: I 122 ILE cc_start: 0.7672 (mt) cc_final: 0.7368 (mt) REVERT: I 153 MET cc_start: 0.6969 (tmm) cc_final: 0.6695 (tmm) REVERT: I 207 GLU cc_start: 0.8297 (tt0) cc_final: 0.7926 (tm-30) REVERT: I 221 LEU cc_start: 0.8332 (mm) cc_final: 0.7482 (tt) REVERT: I 227 MET cc_start: 0.7699 (mtm) cc_final: 0.7294 (mtm) REVERT: I 292 ASP cc_start: 0.8598 (m-30) cc_final: 0.7889 (t0) REVERT: I 330 ILE cc_start: 0.6875 (OUTLIER) cc_final: 0.6653 (pt) REVERT: J 21 TYR cc_start: 0.7267 (t80) cc_final: 0.7047 (t80) REVERT: J 32 CYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5765 (t) REVERT: J 89 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8586 (pmtt) REVERT: J 119 PRO cc_start: 0.8619 (Cg_exo) cc_final: 0.8360 (Cg_endo) REVERT: J 158 THR cc_start: 0.7978 (m) cc_final: 0.7387 (p) REVERT: J 168 LEU cc_start: 0.7364 (tp) cc_final: 0.7122 (tp) REVERT: J 265 SER cc_start: 0.8457 (m) cc_final: 0.7956 (p) REVERT: J 410 TRP cc_start: 0.8452 (m100) cc_final: 0.7493 (m100) REVERT: K 472 HIS cc_start: 0.7794 (t70) cc_final: 0.7411 (t70) outliers start: 61 outliers final: 33 residues processed: 330 average time/residue: 0.1437 time to fit residues: 70.7367 Evaluate side-chains 286 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 249 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR 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 97 LEU Chi-restraints excluded: chain C residue 18 THR 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 75 SER Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 96 THR 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 104 LEU Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 330 ILE 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 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 263 GLN Chi-restraints excluded: chain J residue 296 ASP Chi-restraints excluded: chain J residue 349 ILE Chi-restraints excluded: chain L residue 32 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 76 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 HIS J 422 GLN ** 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 = 0.3922 r_free = 0.3922 target = 0.120443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.091721 restraints weight = 41168.663| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.58 r_work: 0.3293 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19421 Z= 0.203 Angle : 0.670 8.496 27464 Z= 0.369 Chirality : 0.043 0.247 3101 Planarity : 0.005 0.079 2509 Dihedral : 28.444 179.887 4859 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer: Outliers : 5.47 % Allowed : 25.85 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.21), residues: 1572 helix: 0.26 (0.18), residues: 831 sheet: -0.56 (0.46), residues: 111 loop : -1.20 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.026 0.002 TYR G 39 PHE 0.017 0.002 PHE J 210 TRP 0.015 0.002 TRP J 394 HIS 0.009 0.002 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (19421) covalent geometry : angle 0.67036 / 0.37 (27464) hydrogen bonds : bond 0.04982 / 3.43 ( 875) hydrogen bonds : angle 3.96926 / 2.81 ( 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 338 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 264 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.7924 (m-40) cc_final: 0.7664 (m-40) REVERT: D 32 GLU cc_start: 0.7754 (pp20) cc_final: 0.7221 (pp20) REVERT: E 48 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8949 (mp) REVERT: E 58 THR cc_start: 0.8865 (p) cc_final: 0.8648 (p) REVERT: E 94 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8278 (mm-30) REVERT: F 52 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8253 (tp30) REVERT: H 57 SER cc_start: 0.8746 (t) cc_final: 0.8466 (m) REVERT: H 90 GLU cc_start: 0.8422 (mp0) cc_final: 0.8213 (mp0) REVERT: I 122 ILE cc_start: 0.7672 (mt) cc_final: 0.7349 (mt) REVERT: I 207 GLU cc_start: 0.8255 (tt0) cc_final: 0.7908 (tm-30) REVERT: I 221 LEU cc_start: 0.8215 (mm) cc_final: 0.7590 (tt) REVERT: I 227 MET cc_start: 0.7681 (mtm) cc_final: 0.7250 (mtm) REVERT: I 292 ASP cc_start: 0.8628 (m-30) cc_final: 0.8073 (t0) REVERT: I 296 ASN cc_start: 0.7579 (m110) cc_final: 0.7204 (m110) REVERT: J 89 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8570 (pmtt) REVERT: J 227 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6454 (pp20) REVERT: J 265 SER cc_start: 0.8511 (m) cc_final: 0.8072 (p) REVERT: J 410 TRP cc_start: 0.8568 (m100) cc_final: 0.7888 (m100) REVERT: K 471 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8137 (tptt) REVERT: K 472 HIS cc_start: 0.7740 (t70) cc_final: 0.7500 (t70) outliers start: 74 outliers final: 48 residues processed: 315 average time/residue: 0.1434 time to fit residues: 67.9153 Evaluate side-chains 297 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 46 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG 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 109 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 31 LYS 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 G residue 114 VAL 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 148 THR Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 70 ILE 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 175 THR 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 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 349 ILE Chi-restraints excluded: chain K residue 470 GLN 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: 0.7980 chunk 129 optimal weight: 0.0270 chunk 16 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 482 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 = 0.3916 r_free = 0.3916 target = 0.120066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090964 restraints weight = 41468.044| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.68 r_work: 0.3276 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19421 Z= 0.159 Angle : 0.622 8.610 27464 Z= 0.344 Chirality : 0.042 0.265 3101 Planarity : 0.004 0.057 2509 Dihedral : 28.445 179.562 4859 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.01 % Favored : 95.87 % Rotamer: Outliers : 4.73 % Allowed : 25.78 % Favored : 69.50 % 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: -0.28 (0.21), residues: 1572 helix: 0.58 (0.18), residues: 839 sheet: -0.28 (0.47), residues: 115 loop : -1.16 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 469 TYR 0.019 0.002 TYR B 98 PHE 0.016 0.002 PHE L 46 TRP 0.011 0.001 TRP J 394 HIS 0.008 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (19421) covalent geometry : angle 0.62173 / 0.34 (27464) hydrogen bonds : bond 0.04210 / 2.92 ( 875) hydrogen bonds : angle 3.77164 / 2.69 ( 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 319 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8020 (m-40) cc_final: 0.7748 (m-40) REVERT: C 66 GLU cc_start: 0.8175 (tt0) cc_final: 0.7970 (tt0) REVERT: C 95 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8880 (mt) REVERT: D 32 GLU cc_start: 0.7794 (pp20) cc_final: 0.7585 (pp20) REVERT: D 59 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8479 (mmt) REVERT: E 58 THR cc_start: 0.8880 (p) cc_final: 0.8645 (p) REVERT: E 94 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8286 (mm-30) REVERT: F 52 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8175 (tp30) REVERT: G 62 ILE cc_start: 0.8985 (mt) cc_final: 0.8727 (tt) REVERT: H 77 LEU cc_start: 0.9287 (mt) cc_final: 0.9075 (mt) REVERT: H 90 GLU cc_start: 0.8514 (mp0) cc_final: 0.8221 (mp0) REVERT: I 122 ILE cc_start: 0.7522 (mt) cc_final: 0.7186 (mt) REVERT: I 161 HIS cc_start: 0.7590 (m-70) cc_final: 0.6928 (m170) REVERT: I 167 GLU cc_start: 0.7261 (tt0) cc_final: 0.7044 (tt0) REVERT: I 177 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6648 (ptt90) REVERT: I 190 MET cc_start: 0.8687 (pmm) cc_final: 0.8472 (pmm) REVERT: I 207 GLU cc_start: 0.8296 (tt0) cc_final: 0.7941 (tm-30) REVERT: I 221 LEU cc_start: 0.8296 (mm) cc_final: 0.7669 (tt) REVERT: I 227 MET cc_start: 0.7762 (mtm) cc_final: 0.7292 (mtm) REVERT: I 292 ASP cc_start: 0.8675 (m-30) cc_final: 0.8148 (t0) REVERT: I 296 ASN cc_start: 0.7808 (m110) cc_final: 0.7417 (m-40) REVERT: J 32 CYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5998 (t) REVERT: J 82 MET cc_start: 0.6603 (mmm) cc_final: 0.6287 (mtm) REVERT: J 89 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8536 (pmtt) REVERT: J 227 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6605 (pp20) REVERT: J 265 SER cc_start: 0.8606 (m) cc_final: 0.8301 (p) REVERT: J 376 MET cc_start: 0.7690 (pmm) cc_final: 0.7340 (pmm) REVERT: K 471 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8002 (tptt) REVERT: K 472 HIS cc_start: 0.7841 (t70) cc_final: 0.7584 (t70) REVERT: K 506 THR cc_start: 0.8281 (t) cc_final: 0.7911 (p) outliers start: 64 outliers final: 41 residues processed: 298 average time/residue: 0.1528 time to fit residues: 68.0001 Evaluate side-chains 293 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 18 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 59 MET Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 31 LYS 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 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 103 VAL 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 177 ARG Chi-restraints excluded: chain I residue 184 ASP Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 261 LEU 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 180 ILE Chi-restraints excluded: chain J residue 193 VAL Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 263 GLN Chi-restraints excluded: chain J residue 296 ASP 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 470 GLN Chi-restraints excluded: chain L residue 32 GLU 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: 2.9990 chunk 20 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 472 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.117234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088167 restraints weight = 40982.881| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.58 r_work: 0.3223 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19421 Z= 0.201 Angle : 0.660 11.845 27464 Z= 0.358 Chirality : 0.043 0.283 3101 Planarity : 0.005 0.057 2509 Dihedral : 28.554 179.763 4859 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 5.91 % Allowed : 25.26 % Favored : 68.83 % 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: 0.05 (0.21), residues: 1572 helix: 0.88 (0.18), residues: 840 sheet: -0.05 (0.47), residues: 121 loop : -1.09 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 35 TYR 0.022 0.002 TYR B 98 PHE 0.016 0.002 PHE J 99 TRP 0.013 0.002 TRP J 394 HIS 0.009 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (19421) covalent geometry : angle 0.65969 / 0.36 (27464) hydrogen bonds : bond 0.04587 / 3.19 ( 875) hydrogen bonds : angle 3.74691 / 2.67 ( 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 331 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 251 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8226 (m-40) cc_final: 0.8015 (m-40) REVERT: C 95 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8917 (mt) REVERT: D 59 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8481 (mmt) REVERT: E 48 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9033 (mp) REVERT: E 58 THR cc_start: 0.8964 (p) cc_final: 0.8753 (p) REVERT: F 52 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8164 (tp30) REVERT: G 62 ILE cc_start: 0.9009 (mt) cc_final: 0.8776 (tt) REVERT: H 77 LEU cc_start: 0.9318 (mt) cc_final: 0.9100 (mt) REVERT: H 90 GLU cc_start: 0.8436 (mp0) cc_final: 0.8145 (mp0) REVERT: I 122 ILE cc_start: 0.7595 (mt) cc_final: 0.7260 (mt) REVERT: I 161 HIS cc_start: 0.7674 (m-70) cc_final: 0.6941 (m170) REVERT: I 207 GLU cc_start: 0.8290 (tt0) cc_final: 0.7966 (tm-30) REVERT: I 221 LEU cc_start: 0.8286 (mm) cc_final: 0.7750 (tt) REVERT: I 227 MET cc_start: 0.7601 (mtm) cc_final: 0.7207 (mtm) REVERT: I 292 ASP cc_start: 0.8660 (m-30) cc_final: 0.8189 (t0) REVERT: I 296 ASN cc_start: 0.7936 (m110) cc_final: 0.7565 (m-40) REVERT: J 21 TYR cc_start: 0.7646 (t80) cc_final: 0.7446 (t80) REVERT: J 82 MET cc_start: 0.6432 (mmm) cc_final: 0.6144 (mtm) REVERT: J 89 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8556 (pmtt) REVERT: J 195 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8443 (m) REVERT: J 322 MET cc_start: 0.7509 (tpp) cc_final: 0.7228 (tpp) REVERT: J 376 MET cc_start: 0.7753 (pmm) cc_final: 0.7466 (pmm) REVERT: J 394 TRP cc_start: 0.7438 (t60) cc_final: 0.7075 (t60) REVERT: J 410 TRP cc_start: 0.8671 (m100) cc_final: 0.8158 (m100) REVERT: K 471 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7996 (tptt) outliers start: 80 outliers final: 58 residues processed: 308 average time/residue: 0.1477 time to fit residues: 68.6640 Evaluate side-chains 306 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 243 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 29 VAL Chi-restraints excluded: chain C residue 78 THR 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 D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 50 GLU 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 118 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 114 VAL 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 82 MET Chi-restraints excluded: chain I residue 101 HIS Chi-restraints excluded: chain I residue 103 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 I residue 261 LEU 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 32 CYS Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 124 GLU Chi-restraints excluded: chain J residue 165 SER 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 222 MET Chi-restraints excluded: chain J residue 263 GLN Chi-restraints excluded: chain J residue 312 SER Chi-restraints excluded: chain J residue 328 VAL Chi-restraints excluded: chain J residue 349 ILE Chi-restraints excluded: chain J residue 403 LEU Chi-restraints excluded: chain K residue 470 GLN Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 36 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 167 optimal weight: 30.0000 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3892 r_free = 0.3892 target = 0.118636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089779 restraints weight = 41176.986| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.58 r_work: 0.3255 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19421 Z= 0.136 Angle : 0.618 11.813 27464 Z= 0.338 Chirality : 0.042 0.331 3101 Planarity : 0.004 0.055 2509 Dihedral : 28.388 178.078 4859 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 4.28 % Allowed : 25.92 % Favored : 69.79 % 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: 0.33 (0.21), residues: 1572 helix: 1.17 (0.18), residues: 841 sheet: 0.04 (0.46), residues: 121 loop : -1.08 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.017 0.001 TYR F 88 PHE 0.014 0.001 PHE L 46 TRP 0.012 0.001 TRP J 394 HIS 0.007 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (19421) covalent geometry : angle 0.61805 / 0.34 (27464) hydrogen bonds : bond 0.03926 / 2.72 ( 875) hydrogen bonds : angle 3.64605 / 2.60 ( 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 309 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8181 (m-40) cc_final: 0.7974 (m-40) REVERT: C 95 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8837 (mt) REVERT: D 59 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8404 (mmt) REVERT: E 48 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9020 (mp) REVERT: E 58 THR cc_start: 0.8931 (p) cc_final: 0.8716 (p) REVERT: F 52 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8074 (tp30) REVERT: G 62 ILE cc_start: 0.8957 (mt) cc_final: 0.8751 (tt) REVERT: H 90 GLU cc_start: 0.8407 (mp0) cc_final: 0.8141 (mp0) REVERT: I 122 ILE cc_start: 0.7514 (mt) cc_final: 0.7165 (mt) REVERT: I 161 HIS cc_start: 0.7634 (m-70) cc_final: 0.6836 (m170) REVERT: I 207 GLU cc_start: 0.8287 (tt0) cc_final: 0.8018 (tm-30) REVERT: I 221 LEU cc_start: 0.8320 (mm) cc_final: 0.7851 (tt) REVERT: I 227 MET cc_start: 0.7582 (mtm) cc_final: 0.7178 (mtm) REVERT: I 292 ASP cc_start: 0.8666 (m-30) cc_final: 0.8162 (t0) REVERT: I 296 ASN cc_start: 0.7966 (m110) cc_final: 0.7581 (m-40) REVERT: I 355 MET cc_start: 0.5802 (ptt) cc_final: 0.5287 (pmm) REVERT: J 82 MET cc_start: 0.6424 (mmm) cc_final: 0.6006 (mtm) REVERT: J 89 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8521 (pmtt) REVERT: J 227 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6585 (pp20) REVERT: J 322 MET cc_start: 0.7506 (tpp) cc_final: 0.7199 (tpp) REVERT: J 394 TRP cc_start: 0.7318 (t60) cc_final: 0.7038 (t60) REVERT: J 410 TRP cc_start: 0.8598 (m100) cc_final: 0.7941 (m100) REVERT: K 468 ARG cc_start: 0.6890 (tmt170) cc_final: 0.6602 (tmt170) REVERT: K 471 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7949 (tptt) outliers start: 58 outliers final: 39 residues processed: 290 average time/residue: 0.1456 time to fit residues: 64.0609 Evaluate side-chains 283 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 101 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 114 VAL 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 101 HIS 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 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 185 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 89 LYS 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 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 J residue 403 LEU Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain K residue 470 GLN Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 160 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 79 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.118738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.090923 restraints weight = 41364.203| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.59 r_work: 0.3252 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19421 Z= 0.137 Angle : 0.625 10.962 27464 Z= 0.340 Chirality : 0.041 0.325 3101 Planarity : 0.004 0.055 2509 Dihedral : 28.295 178.987 4859 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 4.36 % Allowed : 26.37 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.21), residues: 1572 helix: 1.35 (0.18), residues: 843 sheet: 0.30 (0.49), residues: 115 loop : -1.04 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.015 0.001 TYR B 98 PHE 0.018 0.001 PHE I 279 TRP 0.012 0.001 TRP J 394 HIS 0.007 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (19421) covalent geometry : angle 0.62462 / 0.34 (27464) hydrogen bonds : bond 0.03833 / 2.63 ( 875) hydrogen bonds : angle 3.61792 / 2.57 ( 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 305 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 246 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8186 (m-40) cc_final: 0.7967 (m-40) REVERT: C 95 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8843 (mt) REVERT: C 99 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8637 (mt) REVERT: D 59 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8369 (mmt) REVERT: E 58 THR cc_start: 0.8960 (p) cc_final: 0.8757 (p) REVERT: E 94 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8204 (mm-30) REVERT: F 52 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8035 (tp30) REVERT: G 62 ILE cc_start: 0.8939 (mt) cc_final: 0.8731 (tt) REVERT: H 90 GLU cc_start: 0.8425 (mp0) cc_final: 0.8155 (mp0) REVERT: I 122 ILE cc_start: 0.7509 (mt) cc_final: 0.7159 (mt) REVERT: I 162 THR cc_start: 0.7879 (p) cc_final: 0.7549 (p) REVERT: I 207 GLU cc_start: 0.8384 (tt0) cc_final: 0.8053 (tm-30) REVERT: I 221 LEU cc_start: 0.8354 (mm) cc_final: 0.7888 (tt) REVERT: I 227 MET cc_start: 0.7603 (mtm) cc_final: 0.7262 (mtm) REVERT: I 292 ASP cc_start: 0.8695 (m-30) cc_final: 0.8208 (t0) REVERT: I 296 ASN cc_start: 0.7994 (m110) cc_final: 0.7595 (m-40) REVERT: J 82 MET cc_start: 0.6439 (mmm) cc_final: 0.6032 (mtm) REVERT: J 89 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8423 (pmtt) REVERT: J 92 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7734 (mpp) REVERT: J 195 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8286 (m) REVERT: J 322 MET cc_start: 0.7634 (tpp) cc_final: 0.7104 (tpp) REVERT: J 394 TRP cc_start: 0.7349 (t60) cc_final: 0.6990 (t60) REVERT: J 410 TRP cc_start: 0.8562 (m100) cc_final: 0.7735 (m100) REVERT: K 471 LYS cc_start: 0.8303 (mmtt) cc_final: 0.7997 (tptt) outliers start: 59 outliers final: 42 residues processed: 286 average time/residue: 0.1468 time to fit residues: 63.9269 Evaluate side-chains 286 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 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 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 E residue 71 VAL Chi-restraints excluded: chain E residue 101 VAL 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 114 VAL 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 115 ASN 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 I residue 261 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 92 MET 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 312 SER 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 403 LEU Chi-restraints excluded: chain K residue 470 GLN Chi-restraints excluded: chain L residue 32 GLU Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.118627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090833 restraints weight = 41111.048| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.58 r_work: 0.3253 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19421 Z= 0.137 Angle : 0.635 14.535 27464 Z= 0.341 Chirality : 0.041 0.343 3101 Planarity : 0.004 0.055 2509 Dihedral : 28.234 178.782 4859 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 4.14 % Allowed : 26.96 % Favored : 68.91 % 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: 0.68 (0.22), residues: 1572 helix: 1.50 (0.18), residues: 843 sheet: 0.34 (0.49), residues: 115 loop : -1.00 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.014 0.001 TYR B 98 PHE 0.019 0.001 PHE J 99 TRP 0.013 0.001 TRP J 394 HIS 0.007 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (19421) covalent geometry : angle 0.63459 / 0.34 (27464) hydrogen bonds : bond 0.03759 / 2.58 ( 875) hydrogen bonds : angle 3.59254 / 2.54 ( 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 302 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8196 (m-40) cc_final: 0.7984 (m-40) REVERT: C 95 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8842 (mt) REVERT: C 99 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8616 (mt) REVERT: D 59 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8326 (mmt) REVERT: E 94 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8168 (mm-30) REVERT: F 52 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8021 (tp30) REVERT: H 90 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: I 122 ILE cc_start: 0.7480 (mt) cc_final: 0.7145 (mt) REVERT: I 162 THR cc_start: 0.7891 (p) cc_final: 0.7575 (p) REVERT: I 207 GLU cc_start: 0.8338 (tt0) cc_final: 0.8027 (tm-30) REVERT: I 221 LEU cc_start: 0.8359 (mm) cc_final: 0.7898 (tt) REVERT: I 227 MET cc_start: 0.7614 (mtm) cc_final: 0.7286 (mtm) REVERT: I 292 ASP cc_start: 0.8690 (m-30) cc_final: 0.8204 (t0) REVERT: I 296 ASN cc_start: 0.8030 (m110) cc_final: 0.7624 (m-40) REVERT: J 89 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8369 (pmtt) REVERT: J 195 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8442 (m) REVERT: J 322 MET cc_start: 0.7647 (tpp) cc_final: 0.7310 (tpp) REVERT: J 394 TRP cc_start: 0.7451 (t60) cc_final: 0.6968 (t60) REVERT: J 410 TRP cc_start: 0.8569 (m100) cc_final: 0.7874 (m100) REVERT: K 471 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8008 (tptt) outliers start: 56 outliers final: 41 residues processed: 286 average time/residue: 0.1473 time to fit residues: 63.6533 Evaluate side-chains 289 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 242 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 LEU 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 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 101 VAL 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 114 VAL 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 103 VAL Chi-restraints excluded: chain I residue 115 ASN 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 I residue 261 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 89 LYS 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 312 SER 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 J residue 403 LEU Chi-restraints excluded: chain K residue 470 GLN Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 167 optimal weight: 30.0000 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.118981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.091084 restraints weight = 41196.581| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.65 r_work: 0.3258 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19421 Z= 0.131 Angle : 0.641 14.227 27464 Z= 0.344 Chirality : 0.041 0.355 3101 Planarity : 0.004 0.056 2509 Dihedral : 28.161 178.655 4859 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 3.69 % Allowed : 26.81 % Favored : 69.50 % 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: 0.78 (0.22), residues: 1572 helix: 1.56 (0.18), residues: 849 sheet: 0.35 (0.48), residues: 115 loop : -0.94 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 30 TYR 0.015 0.001 TYR B 98 PHE 0.017 0.001 PHE J 99 TRP 0.015 0.001 TRP J 394 HIS 0.006 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (19421) covalent geometry : angle 0.64147 / 0.34 (27464) hydrogen bonds : bond 0.03670 / 2.51 ( 875) hydrogen bonds : angle 3.58825 / 2.53 ( 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 296 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8148 (m-40) cc_final: 0.7928 (m-40) REVERT: C 95 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8829 (mt) REVERT: C 99 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8602 (mt) REVERT: D 59 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8313 (mmt) REVERT: E 94 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8183 (mm-30) REVERT: F 52 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8016 (tp30) REVERT: H 90 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: I 122 ILE cc_start: 0.7471 (mt) cc_final: 0.7122 (mt) REVERT: I 162 THR cc_start: 0.7892 (p) cc_final: 0.7581 (p) REVERT: I 207 GLU cc_start: 0.8328 (tt0) cc_final: 0.8039 (tm-30) REVERT: I 221 LEU cc_start: 0.8379 (mm) cc_final: 0.7925 (tt) REVERT: I 227 MET cc_start: 0.7620 (mtm) cc_final: 0.7316 (mtm) REVERT: I 292 ASP cc_start: 0.8734 (m-30) cc_final: 0.8253 (t0) REVERT: I 296 ASN cc_start: 0.8021 (m110) cc_final: 0.7624 (m-40) REVERT: J 322 MET cc_start: 0.7645 (tpp) cc_final: 0.7308 (tpp) REVERT: J 394 TRP cc_start: 0.7386 (t60) cc_final: 0.6838 (t60) REVERT: J 410 TRP cc_start: 0.8561 (m100) cc_final: 0.7923 (m100) REVERT: K 469 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8261 (mmm160) outliers start: 50 outliers final: 41 residues processed: 278 average time/residue: 0.1478 time to fit residues: 61.7919 Evaluate side-chains 282 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 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 61 LEU 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 86 SER Chi-restraints excluded: chain E residue 101 VAL 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 114 VAL 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 103 VAL Chi-restraints excluded: chain I residue 115 ASN 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 I residue 261 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL 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 403 LEU Chi-restraints excluded: chain K residue 470 GLN Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 111 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 148 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** 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 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 = 0.3895 r_free = 0.3895 target = 0.118922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090821 restraints weight = 41188.091| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.68 r_work: 0.3251 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19421 Z= 0.132 Angle : 0.648 15.093 27464 Z= 0.345 Chirality : 0.041 0.360 3101 Planarity : 0.004 0.056 2509 Dihedral : 28.135 178.850 4859 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 3.47 % Allowed : 26.74 % Favored : 69.79 % 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: 0.87 (0.22), residues: 1572 helix: 1.66 (0.18), residues: 849 sheet: 0.41 (0.48), residues: 115 loop : -0.96 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 24 TYR 0.029 0.001 TYR H 80 PHE 0.032 0.002 PHE L 46 TRP 0.016 0.001 TRP J 394 HIS 0.006 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (19421) covalent geometry : angle 0.64796 / 0.35 (27464) hydrogen bonds : bond 0.03638 / 2.48 ( 875) hydrogen bonds : angle 3.57994 / 2.52 ( 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 291 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 ASN cc_start: 0.8153 (m-40) cc_final: 0.7924 (m-40) REVERT: C 95 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8807 (mt) REVERT: C 99 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8576 (mt) REVERT: D 59 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8315 (mmt) REVERT: E 94 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8201 (mm-30) REVERT: F 52 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8036 (tp30) REVERT: H 90 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: I 122 ILE cc_start: 0.7237 (mt) cc_final: 0.6901 (mt) REVERT: I 161 HIS cc_start: 0.7718 (m-70) cc_final: 0.7367 (m90) REVERT: I 162 THR cc_start: 0.7926 (p) cc_final: 0.7624 (p) REVERT: I 207 GLU cc_start: 0.8347 (tt0) cc_final: 0.8043 (tm-30) REVERT: I 221 LEU cc_start: 0.8397 (mm) cc_final: 0.7885 (tt) REVERT: I 227 MET cc_start: 0.7727 (mtm) cc_final: 0.7428 (mtm) REVERT: I 269 MET cc_start: 0.8005 (pmm) cc_final: 0.7149 (tmm) REVERT: I 292 ASP cc_start: 0.8808 (m-30) cc_final: 0.8317 (t0) REVERT: I 296 ASN cc_start: 0.8120 (m110) cc_final: 0.7724 (m-40) REVERT: J 122 MET cc_start: 0.8308 (mtm) cc_final: 0.8040 (mtm) REVERT: J 322 MET cc_start: 0.7645 (tpp) cc_final: 0.7335 (tpp) REVERT: J 394 TRP cc_start: 0.7422 (t60) cc_final: 0.6840 (t60) REVERT: J 410 TRP cc_start: 0.8524 (m100) cc_final: 0.7840 (m100) REVERT: K 469 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8223 (mmm160) outliers start: 47 outliers final: 37 residues processed: 275 average time/residue: 0.1397 time to fit residues: 58.2604 Evaluate side-chains 279 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 61 LEU 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 77 LEU 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 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 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 103 VAL Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 129 THR 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 261 LEU Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 32 CYS Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 193 VAL 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 403 LEU Chi-restraints excluded: chain K residue 470 GLN Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS ** 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 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 = 0.3887 r_free = 0.3887 target = 0.118445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.090292 restraints weight = 41340.640| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.71 r_work: 0.3239 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19421 Z= 0.138 Angle : 0.650 15.092 27464 Z= 0.345 Chirality : 0.042 0.362 3101 Planarity : 0.004 0.056 2509 Dihedral : 28.158 178.838 4859 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 3.40 % Allowed : 26.96 % Favored : 69.65 % 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: 0.97 (0.22), residues: 1572 helix: 1.70 (0.18), residues: 850 sheet: 0.64 (0.49), residues: 110 loop : -0.88 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 95 TYR 0.031 0.001 TYR H 80 PHE 0.028 0.001 PHE L 46 TRP 0.019 0.001 TRP J 394 HIS 0.006 0.001 HIS I 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (19421) covalent geometry : angle 0.64988 / 0.35 (27464) hydrogen bonds : bond 0.03692 / 2.53 ( 875) hydrogen bonds : angle 3.56733 / 2.52 ( 2290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5440.72 seconds wall clock time: 93 minutes 34.54 seconds (5614.54 seconds total)