Starting phenix.real_space_refine on Wed Mar 4 23:20:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rd7_4808/03_2026/6rd7_4808.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rd7_4808/03_2026/6rd7_4808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rd7_4808/03_2026/6rd7_4808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rd7_4808/03_2026/6rd7_4808.map" model { file = "/net/cci-nas-00/data/ceres_data/6rd7_4808/03_2026/6rd7_4808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rd7_4808/03_2026/6rd7_4808.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 Zn 1 6.06 5 S 58 5.16 5 C 11231 2.51 5 N 2862 2.21 5 O 3254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17406 Number of models: 1 Model: "" Number of chains: 27 Chain: "0" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 605 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "1" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "5" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "8" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 3.51, per 1000 atoms: 0.20 Number of scatterers: 17406 At special positions: 0 Unit cell: (129.519, 117.936, 221.13, 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) Zn 1 29.99 S 58 16.00 O 3254 8.00 N 2862 7.00 C 11231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 9 69 " - pdb=" SG CYS 9 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 2 sheets defined 79.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain '0' and resid 3 through 10 removed outlier: 3.876A pdb=" N ALA 0 10 " --> pdb=" O TYR 0 6 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 31 removed outlier: 3.666A pdb=" N ALA 0 27 " --> pdb=" O ALA 0 23 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '0' and resid 57 through 61 Processing helix chain '1' and resid 46 through 74 Processing helix chain '1' and resid 83 through 87 Processing helix chain '1' and resid 106 through 143 removed outlier: 3.866A pdb=" N LYS 1 143 " --> pdb=" O ALA 1 139 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 177 Processing helix chain '1' and resid 190 through 205 Processing helix chain '1' and resid 209 through 224 removed outlier: 3.835A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 Processing helix chain '1' and resid 272 through 277 removed outlier: 3.511A pdb=" N VAL 1 277 " --> pdb=" O LEU 1 274 " (cutoff:3.500A) Processing helix chain '1' and resid 281 through 285 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 317 Processing helix chain '1' and resid 318 through 322 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.663A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 363 Processing helix chain '1' and resid 364 through 367 removed outlier: 3.831A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 364 through 367' Processing helix chain '1' and resid 375 through 388 Processing helix chain '1' and resid 392 through 421 removed outlier: 3.583A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY 1 421 " --> pdb=" O LYS 1 417 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.607A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 446 removed outlier: 3.661A pdb=" N ASN 1 446 " --> pdb=" O ASP 1 442 " (cutoff:3.500A) Processing helix chain '1' and resid 446 through 461 Processing helix chain '1' and resid 463 through 479 removed outlier: 3.930A pdb=" N ASP 1 479 " --> pdb=" O GLU 1 475 " (cutoff:3.500A) Processing helix chain '1' and resid 480 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.538A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.635A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '1' and resid 610 through 614 Processing helix chain '3' and resid 78 through 90 Processing helix chain '3' and resid 93 through 98 Processing helix chain '3' and resid 102 through 112 Processing helix chain '3' and resid 117 through 129 removed outlier: 4.211A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 151 Processing helix chain '3' and resid 154 through 168 Processing helix chain '3' and resid 173 through 187 removed outlier: 4.080A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE 3 187 " --> pdb=" O THR 3 183 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 Processing helix chain '3' and resid 215 through 229 Processing helix chain '3' and resid 233 through 242 Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 272 removed outlier: 3.636A pdb=" N ASP 3 259 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 287 removed outlier: 3.605A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 Processing helix chain '5' and resid 7 through 29 removed outlier: 3.537A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 29 through 59 removed outlier: 4.036A pdb=" N THR 5 33 " --> pdb=" O GLN 5 29 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 Processing helix chain '5' and resid 72 through 81 removed outlier: 3.683A pdb=" N VAL 5 76 " --> pdb=" O SER 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 87 through 107 removed outlier: 4.336A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 42 removed outlier: 3.610A pdb=" N THR 6 42 " --> pdb=" O SER 6 38 " (cutoff:3.500A) Processing helix chain '6' and resid 46 through 59 removed outlier: 5.041A pdb=" N LYS 6 52 " --> pdb=" O LEU 6 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR 6 53 " --> pdb=" O SER 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 95 Processing helix chain '6' and resid 98 through 120 removed outlier: 3.658A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '6' and resid 133 through 138 removed outlier: 3.841A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '8' and resid 4 through 9 removed outlier: 3.717A pdb=" N LYS 8 9 " --> pdb=" O VAL 8 6 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 Processing helix chain '8' and resid 31 through 39 removed outlier: 3.557A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 79 removed outlier: 6.881A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 16 Processing helix chain '9' and resid 19 through 24 Processing helix chain '9' and resid 33 through 55 Processing helix chain '9' and resid 76 through 80 Processing helix chain '9' and resid 82 through 96 removed outlier: 4.014A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 70 through 92 Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 92 Processing helix chain 'B' and resid 95 through 126 removed outlier: 3.825A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 70 through 92 Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 70 through 92 Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.827A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 70 through 92 Processing helix chain 'E' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 Processing helix chain 'F' and resid 70 through 92 Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.609A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.827A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 Processing helix chain 'H' and resid 70 through 92 Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.827A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 Processing helix chain 'I' and resid 70 through 92 Processing helix chain 'I' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 Processing helix chain 'J' and resid 70 through 92 Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.826A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 166 removed outlier: 3.638A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 201 removed outlier: 3.637A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 266 removed outlier: 3.964A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN M 243 " --> pdb=" O ARG M 239 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 308 removed outlier: 3.771A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 185 removed outlier: 3.629A pdb=" N LYS 1 183 " --> pdb=" O THR 1 228 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 314 through 317 1337 hydrogen bonds defined for protein. 3933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3486 1.33 - 1.45: 3911 1.45 - 1.57: 10140 1.57 - 1.69: 1 1.69 - 1.81: 97 Bond restraints: 17635 Sorted by residual: bond pdb=" C VAL 3 103 " pdb=" N PRO 3 104 " ideal model delta sigma weight residual 1.335 1.403 -0.068 1.30e-02 5.92e+03 2.74e+01 bond pdb=" C VAL M 222 " pdb=" N PRO M 223 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.36e-02 5.41e+03 2.35e+01 bond pdb=" N THR 9 76 " pdb=" CA THR 9 76 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N CYS 9 69 " pdb=" CA CYS 9 69 " ideal model delta sigma weight residual 1.455 1.485 -0.031 9.60e-03 1.09e+04 1.01e+01 bond pdb=" C LEU 5 31 " pdb=" N PRO 5 32 " ideal model delta sigma weight residual 1.335 1.375 -0.040 1.36e-02 5.41e+03 8.60e+00 ... (remaining 17630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 23304 2.37 - 4.74: 562 4.74 - 7.11: 43 7.11 - 9.48: 17 9.48 - 11.85: 5 Bond angle restraints: 23931 Sorted by residual: angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.37 -7.37 1.10e+00 8.26e-01 4.48e+01 angle pdb=" C ASP 1 106 " pdb=" N VAL 1 107 " pdb=" CA VAL 1 107 " ideal model delta sigma weight residual 120.24 124.41 -4.17 6.30e-01 2.52e+00 4.38e+01 angle pdb=" C ASP 1 91 " pdb=" N TYR 1 92 " pdb=" CA TYR 1 92 " ideal model delta sigma weight residual 120.67 129.25 -8.58 1.34e+00 5.57e-01 4.10e+01 angle pdb=" C VAL 5 71 " pdb=" N SER 5 72 " pdb=" CA SER 5 72 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" N VAL 1 204 " pdb=" CA VAL 1 204 " pdb=" C VAL 1 204 " ideal model delta sigma weight residual 110.62 105.74 4.88 1.02e+00 9.61e-01 2.29e+01 ... (remaining 23926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9492 17.70 - 35.40: 787 35.40 - 53.11: 109 53.11 - 70.81: 35 70.81 - 88.51: 11 Dihedral angle restraints: 10434 sinusoidal: 3836 harmonic: 6598 Sorted by residual: dihedral pdb=" CB CYS 9 69 " pdb=" SG CYS 9 69 " pdb=" SG CYS 9 79 " pdb=" CB CYS 9 79 " ideal model delta sinusoidal sigma weight residual 93.00 178.33 -85.33 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA LYS M 203 " pdb=" C LYS M 203 " pdb=" N PHE M 204 " pdb=" CA PHE M 204 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA VAL 5 71 " pdb=" C VAL 5 71 " pdb=" N SER 5 72 " pdb=" CA SER 5 72 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 10431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2086 0.050 - 0.100: 584 0.100 - 0.149: 139 0.149 - 0.199: 15 0.199 - 0.249: 5 Chirality restraints: 2829 Sorted by residual: chirality pdb=" CA VAL 1 204 " pdb=" N VAL 1 204 " pdb=" C VAL 1 204 " pdb=" CB VAL 1 204 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO 3 77 " pdb=" N PRO 3 77 " pdb=" C PRO 3 77 " pdb=" CB PRO 3 77 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU 1 102 " pdb=" CB LEU 1 102 " pdb=" CD1 LEU 1 102 " pdb=" CD2 LEU 1 102 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2826 not shown) Planarity restraints: 3016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY 9 67 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLY 9 67 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY 9 67 " -0.024 2.00e-02 2.50e+03 pdb=" N MET 9 68 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 108 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C ALA G 108 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA G 108 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU G 109 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 108 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.87e+00 pdb=" C ALA C 108 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA C 108 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU C 109 " -0.016 2.00e-02 2.50e+03 ... (remaining 3013 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 117 2.50 - 3.10: 12472 3.10 - 3.70: 28318 3.70 - 4.30: 41456 4.30 - 4.90: 66132 Nonbonded interactions: 148495 Sorted by model distance: nonbonded pdb=" O ALA E 58 " pdb=" OG SER F 59 " model vdw 1.905 3.040 nonbonded pdb=" CG ARG 1 28 " pdb=" OD1 ASP 1 30 " model vdw 2.017 3.440 nonbonded pdb=" OE2 GLU H 111 " pdb=" CD1 ILE I 113 " model vdw 2.042 3.460 nonbonded pdb=" OE2 GLU F 111 " pdb=" CD1 ILE G 113 " model vdw 2.115 3.460 nonbonded pdb=" OE2 GLU I 111 " pdb=" CD1 ILE J 113 " model vdw 2.139 3.460 ... (remaining 148490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 10.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.310 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 0.007 0.399 17638 Z= 0.338 Angle : 0.894 11.847 23933 Z= 0.545 Chirality : 0.049 0.249 2829 Planarity : 0.009 0.063 3016 Dihedral : 13.556 88.511 6183 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.50 % Favored : 98.28 % Rotamer: Outliers : 0.84 % Allowed : 4.88 % Favored : 94.27 % 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: -1.88 (0.15), residues: 2271 helix: -0.98 (0.11), residues: 1724 sheet: None (None), residues: 0 loop : -1.58 (0.22), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 1 28 TYR 0.032 0.002 TYR 3 153 PHE 0.034 0.002 PHE M 231 TRP 0.015 0.002 TRP 9 73 HIS 0.012 0.001 HIS M 252 Details of bonding type rmsd covalent geometry : bond 0.00638 (17635) covalent geometry : angle 0.89429 (23931) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.95962 ( 2) hydrogen bonds : bond 0.14092 ( 1337) hydrogen bonds : angle 6.10433 ( 3933) metal coordination : bond 0.28424 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 405 time to evaluate : 0.801 Fit side-chains REVERT: 0 34 ARG cc_start: 0.8056 (ptt-90) cc_final: 0.7765 (ptt-90) REVERT: 0 41 GLU cc_start: 0.5947 (pp20) cc_final: 0.5706 (pp20) REVERT: 0 44 ASN cc_start: 0.8678 (m110) cc_final: 0.8240 (m-40) REVERT: 0 60 GLN cc_start: 0.8925 (mm110) cc_final: 0.8705 (mm-40) REVERT: 1 224 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7487 (pptt) REVERT: 1 387 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7512 (mtm-85) REVERT: 1 441 PHE cc_start: 0.8364 (m-80) cc_final: 0.8134 (m-80) REVERT: 1 613 ASP cc_start: 0.8183 (m-30) cc_final: 0.7864 (m-30) REVERT: 3 82 VAL cc_start: 0.3772 (OUTLIER) cc_final: 0.3533 (t) REVERT: 3 151 ASN cc_start: 0.7735 (t0) cc_final: 0.7522 (t160) REVERT: 5 6 GLU cc_start: 0.7817 (tt0) cc_final: 0.7574 (tt0) REVERT: 5 109 GLN cc_start: 0.8595 (mp-120) cc_final: 0.8311 (mm-40) REVERT: 6 86 ILE cc_start: 0.8978 (mt) cc_final: 0.8696 (mm) REVERT: 9 9 LYS cc_start: 0.7264 (ttpt) cc_final: 0.6754 (ttpp) REVERT: 9 68 MET cc_start: 0.7984 (mtm) cc_final: 0.7726 (mtm) REVERT: 9 95 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7571 (mmtp) REVERT: D 92 ASN cc_start: 0.7955 (t0) cc_final: 0.7748 (t0) REVERT: F 81 MET cc_start: 0.8340 (ttp) cc_final: 0.7920 (ttm) REVERT: G 81 MET cc_start: 0.8172 (ttp) cc_final: 0.7826 (ttp) REVERT: G 115 LEU cc_start: 0.7468 (mt) cc_final: 0.7257 (pp) REVERT: H 81 MET cc_start: 0.8582 (ttp) cc_final: 0.8305 (ttp) REVERT: H 102 TYR cc_start: 0.7382 (m-10) cc_final: 0.7134 (m-10) REVERT: I 92 ASN cc_start: 0.8507 (t0) cc_final: 0.8288 (t0) REVERT: I 102 TYR cc_start: 0.7582 (m-10) cc_final: 0.7283 (m-10) REVERT: M 225 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7330 (mm-30) outliers start: 15 outliers final: 5 residues processed: 419 average time/residue: 0.5125 time to fit residues: 243.2632 Evaluate side-chains 287 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 281 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 203 SER Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain J residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 100 GLN 1 316 ASN 1 428 HIS 1 482 ASN 1 492 GLN 1 562 ASN ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 179 GLN 3 206 ASN 3 269 GLN 5 29 GLN 6 40 ASN 8 26 HIS 8 29 GLN 9 35 GLN 9 50 ASN 9 60 ASN F 87 ASN J 87 ASN J 98 GLN M 108 ASN M 163 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.132878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093450 restraints weight = 22051.516| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.66 r_work: 0.2875 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17638 Z= 0.167 Angle : 0.546 7.456 23933 Z= 0.287 Chirality : 0.038 0.138 2829 Planarity : 0.005 0.052 3016 Dihedral : 4.611 28.102 2417 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.55 % Rotamer: Outliers : 2.81 % Allowed : 12.97 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2271 helix: 0.65 (0.12), residues: 1738 sheet: None (None), residues: 0 loop : -0.62 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 453 TYR 0.017 0.002 TYR 5 51 PHE 0.018 0.002 PHE D 116 TRP 0.013 0.002 TRP 5 21 HIS 0.011 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00366 (17635) covalent geometry : angle 0.54576 (23931) SS BOND : bond 0.00737 ( 1) SS BOND : angle 2.79444 ( 2) hydrogen bonds : bond 0.05193 ( 1337) hydrogen bonds : angle 4.12852 ( 3933) metal coordination : bond 0.00741 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 311 time to evaluate : 0.548 Fit side-chains REVERT: 0 34 ARG cc_start: 0.8251 (ptt-90) cc_final: 0.7749 (ptt-90) REVERT: 0 44 ASN cc_start: 0.8677 (m110) cc_final: 0.8372 (m-40) REVERT: 1 34 GLU cc_start: 0.5593 (tp30) cc_final: 0.5251 (pm20) REVERT: 1 224 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7421 (pptt) REVERT: 1 233 VAL cc_start: 0.8508 (t) cc_final: 0.8294 (p) REVERT: 1 387 ARG cc_start: 0.8244 (mtp180) cc_final: 0.7677 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: 1 441 PHE cc_start: 0.8182 (m-80) cc_final: 0.7913 (m-80) REVERT: 1 452 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7587 (tm-30) REVERT: 1 501 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7946 (mm-30) REVERT: 3 291 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: 5 6 GLU cc_start: 0.8433 (tt0) cc_final: 0.8071 (tt0) REVERT: 5 112 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8320 (ptm160) REVERT: 6 37 LYS cc_start: 0.8844 (tttp) cc_final: 0.8610 (tttm) REVERT: 6 86 ILE cc_start: 0.8982 (mt) cc_final: 0.8643 (mm) REVERT: 6 98 GLU cc_start: 0.7915 (pt0) cc_final: 0.7635 (mt-10) REVERT: 9 9 LYS cc_start: 0.7037 (ttpt) cc_final: 0.6424 (ttpp) REVERT: 9 50 ASN cc_start: 0.8518 (m-40) cc_final: 0.8259 (m110) REVERT: 9 95 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7529 (mmtp) REVERT: C 91 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7343 (mtp85) REVERT: C 122 PHE cc_start: 0.6913 (m-10) cc_final: 0.6576 (t80) REVERT: D 92 ASN cc_start: 0.8035 (t0) cc_final: 0.7625 (t0) REVERT: D 94 ASN cc_start: 0.7122 (m-40) cc_final: 0.6719 (m110) REVERT: F 91 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7845 (ttm-80) REVERT: F 92 ASN cc_start: 0.8464 (t0) cc_final: 0.8169 (t0) REVERT: G 81 MET cc_start: 0.8391 (ttp) cc_final: 0.8026 (ttp) REVERT: H 61 MET cc_start: 0.8194 (mmt) cc_final: 0.7882 (mtp) REVERT: H 81 MET cc_start: 0.8690 (ttp) cc_final: 0.8444 (ttp) REVERT: H 102 TYR cc_start: 0.7640 (m-10) cc_final: 0.7383 (m-10) REVERT: I 92 ASN cc_start: 0.8414 (t0) cc_final: 0.8202 (t0) REVERT: I 102 TYR cc_start: 0.7908 (m-10) cc_final: 0.7557 (m-10) REVERT: M 270 MET cc_start: 0.6638 (ttm) cc_final: 0.6383 (ttt) outliers start: 50 outliers final: 18 residues processed: 339 average time/residue: 0.5274 time to fit residues: 202.0058 Evaluate side-chains 295 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 415 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 291 GLU Chi-restraints excluded: chain 3 residue 293 SER Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 116 optimal weight: 0.0570 chunk 206 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 52 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 298 GLN 1 379 GLN 1 428 HIS ** 3 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 189 HIS 3 256 GLN 3 269 GLN 9 35 GLN F 87 ASN J 98 GLN M 121 ASN M 243 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.094301 restraints weight = 22096.177| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.67 r_work: 0.2887 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17638 Z= 0.132 Angle : 0.495 7.803 23933 Z= 0.257 Chirality : 0.036 0.127 2829 Planarity : 0.004 0.053 3016 Dihedral : 4.149 27.826 2411 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.72 % Favored : 98.24 % Rotamer: Outliers : 2.75 % Allowed : 14.21 % Favored : 83.04 % 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: 1.48 (0.17), residues: 2271 helix: 1.40 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : -0.23 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 91 TYR 0.023 0.001 TYR G 102 PHE 0.015 0.001 PHE 1 529 TRP 0.012 0.001 TRP 5 21 HIS 0.011 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00278 (17635) covalent geometry : angle 0.49358 (23931) SS BOND : bond 0.00321 ( 1) SS BOND : angle 4.07657 ( 2) hydrogen bonds : bond 0.04587 ( 1337) hydrogen bonds : angle 3.80005 ( 3933) metal coordination : bond 0.00154 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 0.644 Fit side-chains REVERT: 0 41 GLU cc_start: 0.5197 (pp20) cc_final: 0.4457 (pm20) REVERT: 0 44 ASN cc_start: 0.8709 (m110) cc_final: 0.8440 (m-40) REVERT: 1 34 GLU cc_start: 0.5662 (tp30) cc_final: 0.5125 (pm20) REVERT: 1 143 LYS cc_start: 0.8305 (ptpp) cc_final: 0.7554 (pttp) REVERT: 1 194 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7109 (ttmp) REVERT: 1 224 LYS cc_start: 0.8523 (mtmm) cc_final: 0.7387 (pptt) REVERT: 1 233 VAL cc_start: 0.8628 (t) cc_final: 0.8427 (p) REVERT: 1 387 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7667 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8200 (tt0) cc_final: 0.7825 (tm-30) REVERT: 1 441 PHE cc_start: 0.8074 (m-80) cc_final: 0.7834 (m-80) REVERT: 1 452 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7623 (tm-30) REVERT: 1 501 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7959 (mm-30) REVERT: 3 126 GLU cc_start: 0.8345 (mp0) cc_final: 0.8014 (mp0) REVERT: 3 151 ASN cc_start: 0.8403 (t0) cc_final: 0.8106 (t160) REVERT: 3 314 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7240 (tp30) REVERT: 6 37 LYS cc_start: 0.8865 (tttp) cc_final: 0.8607 (tttm) REVERT: 6 86 ILE cc_start: 0.8957 (mt) cc_final: 0.8638 (mm) REVERT: 9 9 LYS cc_start: 0.6951 (ttpt) cc_final: 0.6362 (ttpp) REVERT: 9 28 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.7329 (ptp90) REVERT: 9 95 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7545 (mmtp) REVERT: C 122 PHE cc_start: 0.6876 (m-10) cc_final: 0.6642 (t80) REVERT: D 94 ASN cc_start: 0.7403 (m-40) cc_final: 0.7154 (m110) REVERT: D 119 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7445 (tm) REVERT: F 91 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7783 (ttm-80) REVERT: F 92 ASN cc_start: 0.8565 (t0) cc_final: 0.8222 (t0) REVERT: G 81 MET cc_start: 0.8426 (ttp) cc_final: 0.8085 (ttp) REVERT: H 81 MET cc_start: 0.8620 (ttp) cc_final: 0.8367 (ttp) REVERT: H 102 TYR cc_start: 0.7662 (m-10) cc_final: 0.7438 (m-10) REVERT: I 102 TYR cc_start: 0.7926 (m-10) cc_final: 0.7653 (m-10) REVERT: M 225 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7533 (mm-30) REVERT: M 251 LEU cc_start: 0.9134 (tp) cc_final: 0.8902 (mt) outliers start: 49 outliers final: 15 residues processed: 324 average time/residue: 0.5449 time to fit residues: 198.5609 Evaluate side-chains 291 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 136 GLU Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 194 LYS Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 293 SER Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain M residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 89 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 192 optimal weight: 0.4980 chunk 175 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 101 ASN 1 379 GLN 1 394 GLN 1 428 HIS 1 430 GLN 3 256 GLN 3 269 GLN 9 35 GLN 9 50 ASN F 87 ASN G 92 ASN G 98 GLN J 98 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097991 restraints weight = 22544.011| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.51 r_work: 0.2948 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17638 Z= 0.153 Angle : 0.506 8.361 23933 Z= 0.261 Chirality : 0.037 0.153 2829 Planarity : 0.004 0.054 3016 Dihedral : 4.107 26.971 2411 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.89 % Favored : 98.06 % Rotamer: Outliers : 2.98 % Allowed : 14.71 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.18), residues: 2271 helix: 1.68 (0.12), residues: 1733 sheet: None (None), residues: 0 loop : -0.06 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 1 453 TYR 0.023 0.002 TYR J 102 PHE 0.014 0.001 PHE 1 529 TRP 0.012 0.001 TRP 5 21 HIS 0.011 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00340 (17635) covalent geometry : angle 0.50422 (23931) SS BOND : bond 0.00428 ( 1) SS BOND : angle 5.00253 ( 2) hydrogen bonds : bond 0.04624 ( 1337) hydrogen bonds : angle 3.74869 ( 3933) metal coordination : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 287 time to evaluate : 0.664 Fit side-chains REVERT: 0 41 GLU cc_start: 0.4945 (OUTLIER) cc_final: 0.4324 (pm20) REVERT: 0 44 ASN cc_start: 0.8747 (m110) cc_final: 0.8491 (m-40) REVERT: 1 34 GLU cc_start: 0.5989 (tp30) cc_final: 0.5153 (pm20) REVERT: 1 194 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7147 (ttmp) REVERT: 1 195 LYS cc_start: 0.7879 (mmmm) cc_final: 0.7457 (pttm) REVERT: 1 224 LYS cc_start: 0.8604 (mtmm) cc_final: 0.7462 (pptt) REVERT: 1 387 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7776 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8208 (tt0) cc_final: 0.7905 (tm-30) REVERT: 1 441 PHE cc_start: 0.8136 (m-80) cc_final: 0.7905 (m-80) REVERT: 1 452 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7669 (tm-30) REVERT: 1 501 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8009 (mm-30) REVERT: 3 314 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7372 (tp30) REVERT: 5 112 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8544 (ptm-80) REVERT: 6 37 LYS cc_start: 0.8890 (tttp) cc_final: 0.8689 (tttm) REVERT: 6 86 ILE cc_start: 0.9028 (mt) cc_final: 0.8708 (mm) REVERT: 9 9 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6581 (ttpp) REVERT: 9 32 SER cc_start: 0.7864 (t) cc_final: 0.7548 (p) REVERT: 9 35 GLN cc_start: 0.8309 (mt0) cc_final: 0.7971 (mt0) REVERT: A 91 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7458 (ttp-110) REVERT: C 122 PHE cc_start: 0.7033 (m-10) cc_final: 0.6797 (t80) REVERT: D 94 ASN cc_start: 0.7809 (m-40) cc_final: 0.7548 (m110) REVERT: D 119 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7554 (tm) REVERT: F 92 ASN cc_start: 0.8647 (t0) cc_final: 0.8321 (t0) REVERT: H 61 MET cc_start: 0.8103 (mmt) cc_final: 0.7850 (mtp) REVERT: H 81 MET cc_start: 0.8675 (ttp) cc_final: 0.8435 (ttp) REVERT: H 102 TYR cc_start: 0.7808 (m-10) cc_final: 0.7554 (m-10) REVERT: I 92 ASN cc_start: 0.8585 (t0) cc_final: 0.8373 (t0) REVERT: J 59 SER cc_start: 0.9033 (m) cc_final: 0.8637 (p) REVERT: M 225 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7650 (mm-30) REVERT: M 251 LEU cc_start: 0.9217 (tp) cc_final: 0.8973 (mt) outliers start: 53 outliers final: 25 residues processed: 319 average time/residue: 0.5262 time to fit residues: 189.4958 Evaluate side-chains 303 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 136 GLU Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 194 LYS Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 182 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 55 GLN 1 101 ASN 1 428 HIS 3 256 GLN 3 269 GLN F 87 ASN G 92 ASN J 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.132853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.097134 restraints weight = 22441.998| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.52 r_work: 0.2868 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17638 Z= 0.164 Angle : 0.511 8.479 23933 Z= 0.263 Chirality : 0.037 0.119 2829 Planarity : 0.004 0.056 3016 Dihedral : 4.118 26.812 2411 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 3.26 % Allowed : 15.16 % Favored : 81.58 % 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: 2.04 (0.18), residues: 2271 helix: 1.80 (0.12), residues: 1732 sheet: None (None), residues: 0 loop : -0.01 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 91 TYR 0.025 0.002 TYR A 102 PHE 0.014 0.001 PHE 1 529 TRP 0.011 0.001 TRP 5 21 HIS 0.010 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00371 (17635) covalent geometry : angle 0.50991 (23931) SS BOND : bond 0.00036 ( 1) SS BOND : angle 4.07304 ( 2) hydrogen bonds : bond 0.04637 ( 1337) hydrogen bonds : angle 3.73992 ( 3933) metal coordination : bond 0.00190 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 287 time to evaluate : 0.681 Fit side-chains REVERT: 0 41 GLU cc_start: 0.4796 (OUTLIER) cc_final: 0.4214 (pm20) REVERT: 0 44 ASN cc_start: 0.8722 (m110) cc_final: 0.8474 (m-40) REVERT: 1 34 GLU cc_start: 0.5866 (tp30) cc_final: 0.4793 (pm20) REVERT: 1 143 LYS cc_start: 0.8555 (ptpp) cc_final: 0.7813 (pttp) REVERT: 1 195 LYS cc_start: 0.7833 (mmmm) cc_final: 0.7369 (pttm) REVERT: 1 224 LYS cc_start: 0.8585 (mtmm) cc_final: 0.7434 (pptt) REVERT: 1 387 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7684 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8153 (tt0) cc_final: 0.7787 (tm-30) REVERT: 1 438 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8271 (tp-100) REVERT: 1 441 PHE cc_start: 0.8103 (m-80) cc_final: 0.7789 (m-80) REVERT: 1 452 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7599 (tm-30) REVERT: 1 501 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7961 (mm-30) REVERT: 3 98 VAL cc_start: 0.6155 (OUTLIER) cc_final: 0.5722 (t) REVERT: 3 151 ASN cc_start: 0.8553 (t0) cc_final: 0.8228 (t160) REVERT: 3 314 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7247 (tp30) REVERT: 5 112 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8533 (ptm-80) REVERT: 6 37 LYS cc_start: 0.8874 (tttp) cc_final: 0.8633 (tttm) REVERT: 6 86 ILE cc_start: 0.8978 (mt) cc_final: 0.8669 (mm) REVERT: 9 9 LYS cc_start: 0.7103 (ttpt) cc_final: 0.6487 (ttpp) REVERT: 9 32 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7392 (p) REVERT: 9 50 ASN cc_start: 0.8614 (m-40) cc_final: 0.8343 (m110) REVERT: A 91 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7390 (ttp-110) REVERT: B 81 MET cc_start: 0.9000 (ttp) cc_final: 0.8600 (ttp) REVERT: C 122 PHE cc_start: 0.6891 (m-10) cc_final: 0.6636 (t80) REVERT: D 94 ASN cc_start: 0.7908 (m-40) cc_final: 0.7636 (m110) REVERT: D 119 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7410 (tm) REVERT: F 92 ASN cc_start: 0.8627 (t0) cc_final: 0.8294 (t0) REVERT: H 61 MET cc_start: 0.8039 (mmt) cc_final: 0.7736 (mtp) REVERT: H 81 MET cc_start: 0.8528 (ttp) cc_final: 0.8281 (ttp) REVERT: H 102 TYR cc_start: 0.7847 (m-10) cc_final: 0.7627 (m-10) REVERT: I 92 ASN cc_start: 0.8574 (t0) cc_final: 0.8306 (t0) REVERT: J 66 CYS cc_start: 0.8523 (m) cc_final: 0.8097 (m) REVERT: M 225 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7613 (mm-30) REVERT: M 251 LEU cc_start: 0.9139 (tp) cc_final: 0.8876 (mt) outliers start: 58 outliers final: 29 residues processed: 319 average time/residue: 0.5093 time to fit residues: 183.9295 Evaluate side-chains 311 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 101 ASN Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 199 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 101 ASN 1 379 GLN 1 428 HIS 3 256 GLN 3 269 GLN 9 35 GLN C 98 GLN E 98 GLN F 87 ASN J 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.097201 restraints weight = 22454.964| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.51 r_work: 0.2871 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17638 Z= 0.152 Angle : 0.502 8.596 23933 Z= 0.258 Chirality : 0.037 0.159 2829 Planarity : 0.004 0.056 3016 Dihedral : 4.073 27.047 2411 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 2.70 % Allowed : 16.11 % Favored : 81.19 % 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: 2.20 (0.18), residues: 2271 helix: 1.91 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : 0.04 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 91 TYR 0.026 0.002 TYR A 102 PHE 0.017 0.001 PHE 9 29 TRP 0.011 0.001 TRP 9 73 HIS 0.011 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00339 (17635) covalent geometry : angle 0.50139 (23931) SS BOND : bond 0.00226 ( 1) SS BOND : angle 3.35725 ( 2) hydrogen bonds : bond 0.04531 ( 1337) hydrogen bonds : angle 3.70398 ( 3933) metal coordination : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 0.693 Fit side-chains REVERT: 0 41 GLU cc_start: 0.4668 (OUTLIER) cc_final: 0.3967 (pm20) REVERT: 1 34 GLU cc_start: 0.5644 (tp30) cc_final: 0.4758 (pm20) REVERT: 1 195 LYS cc_start: 0.7828 (mmmm) cc_final: 0.7360 (pttm) REVERT: 1 212 GLU cc_start: 0.7233 (mp0) cc_final: 0.7013 (mp0) REVERT: 1 224 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7378 (pptt) REVERT: 1 387 ARG cc_start: 0.8247 (mtp180) cc_final: 0.7678 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8163 (tt0) cc_final: 0.7805 (tm-30) REVERT: 1 438 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8272 (tp-100) REVERT: 1 441 PHE cc_start: 0.8102 (m-80) cc_final: 0.7741 (m-80) REVERT: 1 452 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7606 (tm-30) REVERT: 1 501 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7990 (mm-30) REVERT: 3 98 VAL cc_start: 0.6219 (OUTLIER) cc_final: 0.5805 (t) REVERT: 3 151 ASN cc_start: 0.8549 (t0) cc_final: 0.8275 (t160) REVERT: 6 37 LYS cc_start: 0.8849 (tttp) cc_final: 0.8618 (tttm) REVERT: 6 86 ILE cc_start: 0.8964 (mt) cc_final: 0.8659 (mm) REVERT: 9 9 LYS cc_start: 0.7071 (ttpt) cc_final: 0.6493 (ttpp) REVERT: 9 32 SER cc_start: 0.7697 (OUTLIER) cc_final: 0.7339 (p) REVERT: B 81 MET cc_start: 0.9042 (ttp) cc_final: 0.8644 (ttp) REVERT: C 122 PHE cc_start: 0.6896 (m-10) cc_final: 0.6655 (t80) REVERT: D 94 ASN cc_start: 0.7966 (m-40) cc_final: 0.7707 (m110) REVERT: D 119 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7447 (tm) REVERT: F 92 ASN cc_start: 0.8606 (t0) cc_final: 0.8254 (t0) REVERT: H 61 MET cc_start: 0.7986 (mmt) cc_final: 0.7670 (mtp) REVERT: H 81 MET cc_start: 0.8523 (ttp) cc_final: 0.8282 (ttp) REVERT: H 102 TYR cc_start: 0.7824 (m-10) cc_final: 0.7603 (m-10) REVERT: I 92 ASN cc_start: 0.8579 (t0) cc_final: 0.8313 (t0) REVERT: I 102 TYR cc_start: 0.8026 (m-10) cc_final: 0.7811 (m-10) REVERT: J 66 CYS cc_start: 0.8502 (m) cc_final: 0.8062 (m) REVERT: M 251 LEU cc_start: 0.9136 (tp) cc_final: 0.8892 (mt) outliers start: 48 outliers final: 29 residues processed: 306 average time/residue: 0.5202 time to fit residues: 180.3816 Evaluate side-chains 305 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain M residue 110 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 212 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 213 optimal weight: 0.0040 chunk 119 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 101 ASN 1 428 HIS 3 256 GLN 3 269 GLN 9 35 GLN 9 50 ASN E 98 GLN F 87 ASN G 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097064 restraints weight = 22402.162| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.58 r_work: 0.2849 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17638 Z= 0.163 Angle : 0.509 9.210 23933 Z= 0.262 Chirality : 0.037 0.120 2829 Planarity : 0.004 0.056 3016 Dihedral : 4.079 26.874 2411 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.89 % Favored : 98.06 % Rotamer: Outliers : 2.86 % Allowed : 16.56 % Favored : 80.57 % 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: 2.26 (0.18), residues: 2271 helix: 1.96 (0.12), residues: 1732 sheet: None (None), residues: 0 loop : 0.06 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 91 TYR 0.030 0.002 TYR A 102 PHE 0.014 0.001 PHE 1 529 TRP 0.011 0.001 TRP 5 21 HIS 0.011 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00369 (17635) covalent geometry : angle 0.50877 (23931) SS BOND : bond 0.00158 ( 1) SS BOND : angle 2.07420 ( 2) hydrogen bonds : bond 0.04589 ( 1337) hydrogen bonds : angle 3.72464 ( 3933) metal coordination : bond 0.00183 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.731 Fit side-chains REVERT: 0 41 GLU cc_start: 0.4649 (OUTLIER) cc_final: 0.3822 (pm20) REVERT: 1 34 GLU cc_start: 0.5717 (tp30) cc_final: 0.4697 (pm20) REVERT: 1 194 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7147 (ttmp) REVERT: 1 195 LYS cc_start: 0.7850 (mmmm) cc_final: 0.7344 (pttm) REVERT: 1 224 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7367 (pptt) REVERT: 1 387 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7653 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8154 (tt0) cc_final: 0.7771 (tm-30) REVERT: 1 438 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8271 (tp-100) REVERT: 1 441 PHE cc_start: 0.8062 (m-80) cc_final: 0.7682 (m-80) REVERT: 1 452 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7556 (tm-30) REVERT: 1 501 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7986 (mm-30) REVERT: 3 98 VAL cc_start: 0.6130 (OUTLIER) cc_final: 0.5722 (t) REVERT: 3 151 ASN cc_start: 0.8580 (t0) cc_final: 0.8284 (t160) REVERT: 3 314 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7149 (tp30) REVERT: 5 112 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8553 (ptm-80) REVERT: 6 37 LYS cc_start: 0.8850 (tttp) cc_final: 0.8605 (tttm) REVERT: 6 86 ILE cc_start: 0.8939 (mt) cc_final: 0.8631 (mm) REVERT: 9 9 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6545 (ttpp) REVERT: 9 32 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7378 (p) REVERT: B 81 MET cc_start: 0.9038 (ttp) cc_final: 0.8614 (ttp) REVERT: C 122 PHE cc_start: 0.6864 (m-10) cc_final: 0.6633 (t80) REVERT: D 94 ASN cc_start: 0.7981 (m-40) cc_final: 0.7694 (m110) REVERT: D 119 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7400 (tm) REVERT: F 92 ASN cc_start: 0.8632 (t0) cc_final: 0.8268 (t0) REVERT: H 61 MET cc_start: 0.7977 (mmt) cc_final: 0.7682 (mtp) REVERT: H 81 MET cc_start: 0.8519 (ttp) cc_final: 0.8272 (ttp) REVERT: I 92 ASN cc_start: 0.8575 (t0) cc_final: 0.8289 (t0) REVERT: I 102 TYR cc_start: 0.8030 (m-10) cc_final: 0.7758 (m-10) REVERT: J 66 CYS cc_start: 0.8510 (m) cc_final: 0.8074 (m) REVERT: J 111 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: M 251 LEU cc_start: 0.9099 (tp) cc_final: 0.8844 (mt) outliers start: 51 outliers final: 30 residues processed: 305 average time/residue: 0.5175 time to fit residues: 178.2765 Evaluate side-chains 305 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 101 ASN Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 194 LYS Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 255 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 59 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 105 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 428 HIS 3 256 GLN 3 269 GLN 6 57 GLN 9 35 GLN A 92 ASN E 98 GLN F 87 ASN G 98 GLN J 98 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098319 restraints weight = 22493.094| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.57 r_work: 0.2855 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17638 Z= 0.134 Angle : 0.495 9.954 23933 Z= 0.255 Chirality : 0.036 0.153 2829 Planarity : 0.004 0.056 3016 Dihedral : 4.028 27.326 2411 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 2.53 % Allowed : 17.13 % Favored : 80.35 % 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: 2.41 (0.18), residues: 2271 helix: 2.07 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : 0.12 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 91 TYR 0.032 0.002 TYR A 102 PHE 0.029 0.001 PHE 9 29 TRP 0.011 0.001 TRP 1 583 HIS 0.011 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00290 (17635) covalent geometry : angle 0.49437 (23931) SS BOND : bond 0.00123 ( 1) SS BOND : angle 2.85161 ( 2) hydrogen bonds : bond 0.04378 ( 1337) hydrogen bonds : angle 3.66242 ( 3933) metal coordination : bond 0.00144 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.4517 (OUTLIER) cc_final: 0.3720 (pm20) REVERT: 1 34 GLU cc_start: 0.5620 (tp30) cc_final: 0.4660 (pm20) REVERT: 1 224 LYS cc_start: 0.8547 (mtmm) cc_final: 0.7329 (pptt) REVERT: 1 387 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7610 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8090 (tt0) cc_final: 0.7785 (tm-30) REVERT: 1 438 GLN cc_start: 0.8454 (tp-100) cc_final: 0.8211 (tp-100) REVERT: 1 441 PHE cc_start: 0.8053 (m-80) cc_final: 0.7647 (m-80) REVERT: 1 452 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7521 (tm-30) REVERT: 1 501 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7937 (mm-30) REVERT: 3 98 VAL cc_start: 0.6368 (OUTLIER) cc_final: 0.5978 (t) REVERT: 3 151 ASN cc_start: 0.8554 (t0) cc_final: 0.8233 (t160) REVERT: 3 314 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7110 (tp30) REVERT: 5 112 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8525 (ptm-80) REVERT: 6 37 LYS cc_start: 0.8790 (tttp) cc_final: 0.8541 (tttm) REVERT: 6 86 ILE cc_start: 0.8905 (mt) cc_final: 0.8615 (mm) REVERT: 9 9 LYS cc_start: 0.7062 (ttpt) cc_final: 0.6423 (ttpp) REVERT: 9 32 SER cc_start: 0.7754 (t) cc_final: 0.7342 (p) REVERT: B 81 MET cc_start: 0.9008 (ttp) cc_final: 0.8584 (ttp) REVERT: B 115 LEU cc_start: 0.7949 (mp) cc_final: 0.7725 (mm) REVERT: C 122 PHE cc_start: 0.6876 (m-10) cc_final: 0.6630 (t80) REVERT: D 94 ASN cc_start: 0.7974 (m-40) cc_final: 0.7640 (m110) REVERT: D 119 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7367 (tm) REVERT: F 92 ASN cc_start: 0.8620 (t0) cc_final: 0.8253 (t0) REVERT: H 61 MET cc_start: 0.7917 (mmt) cc_final: 0.7655 (mtp) REVERT: H 81 MET cc_start: 0.8481 (ttp) cc_final: 0.8240 (ttp) REVERT: I 92 ASN cc_start: 0.8549 (t0) cc_final: 0.8267 (t0) REVERT: I 102 TYR cc_start: 0.8131 (m-10) cc_final: 0.7891 (m-10) REVERT: J 66 CYS cc_start: 0.8509 (m) cc_final: 0.8074 (m) REVERT: J 111 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: M 251 LEU cc_start: 0.9079 (tp) cc_final: 0.8847 (mt) REVERT: M 270 MET cc_start: 0.6314 (ttm) cc_final: 0.6055 (ttm) outliers start: 45 outliers final: 29 residues processed: 307 average time/residue: 0.5043 time to fit residues: 175.9469 Evaluate side-chains 303 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 269 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 72 SER Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 174 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 206 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 221 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 428 HIS 3 256 GLN 3 269 GLN 6 57 GLN 9 35 GLN E 98 GLN F 87 ASN G 92 ASN G 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.098220 restraints weight = 22487.144| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.57 r_work: 0.2850 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17638 Z= 0.142 Angle : 0.504 10.361 23933 Z= 0.259 Chirality : 0.037 0.147 2829 Planarity : 0.003 0.056 3016 Dihedral : 4.013 26.963 2411 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 2.41 % Allowed : 17.80 % Favored : 79.79 % 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: 2.46 (0.18), residues: 2271 helix: 2.10 (0.12), residues: 1737 sheet: None (None), residues: 0 loop : 0.14 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 91 TYR 0.037 0.002 TYR A 102 PHE 0.013 0.001 PHE 1 529 TRP 0.011 0.001 TRP 5 21 HIS 0.011 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00311 (17635) covalent geometry : angle 0.50320 (23931) SS BOND : bond 0.00201 ( 1) SS BOND : angle 2.64892 ( 2) hydrogen bonds : bond 0.04423 ( 1337) hydrogen bonds : angle 3.66592 ( 3933) metal coordination : bond 0.00155 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.4526 (OUTLIER) cc_final: 0.3739 (pm20) REVERT: 1 34 GLU cc_start: 0.5661 (tp30) cc_final: 0.4653 (pm20) REVERT: 1 224 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7290 (pptt) REVERT: 1 387 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7615 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8086 (tt0) cc_final: 0.7776 (tm-30) REVERT: 1 438 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8207 (tp-100) REVERT: 1 441 PHE cc_start: 0.8032 (m-80) cc_final: 0.7617 (m-80) REVERT: 1 452 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7516 (tm-30) REVERT: 1 501 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7937 (mm-30) REVERT: 3 98 VAL cc_start: 0.6495 (OUTLIER) cc_final: 0.6111 (t) REVERT: 3 151 ASN cc_start: 0.8572 (t0) cc_final: 0.8286 (t160) REVERT: 3 314 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7129 (tp30) REVERT: 5 112 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8529 (ptm-80) REVERT: 6 37 LYS cc_start: 0.8814 (tttp) cc_final: 0.8572 (tttm) REVERT: 9 9 LYS cc_start: 0.7049 (ttpt) cc_final: 0.6472 (ttpp) REVERT: 9 32 SER cc_start: 0.7748 (OUTLIER) cc_final: 0.7323 (p) REVERT: B 81 MET cc_start: 0.9018 (ttp) cc_final: 0.8565 (ttp) REVERT: B 115 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 122 PHE cc_start: 0.6869 (m-10) cc_final: 0.6616 (t80) REVERT: D 94 ASN cc_start: 0.7952 (m-40) cc_final: 0.7608 (m110) REVERT: D 119 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7334 (tm) REVERT: F 92 ASN cc_start: 0.8628 (t0) cc_final: 0.8247 (t0) REVERT: H 81 MET cc_start: 0.8477 (ttp) cc_final: 0.8240 (ttp) REVERT: I 92 ASN cc_start: 0.8572 (t0) cc_final: 0.8322 (t0) REVERT: I 102 TYR cc_start: 0.8191 (m-10) cc_final: 0.7976 (m-10) REVERT: J 66 CYS cc_start: 0.8484 (m) cc_final: 0.8041 (m) REVERT: J 111 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: M 251 LEU cc_start: 0.9065 (tp) cc_final: 0.8827 (mt) outliers start: 43 outliers final: 29 residues processed: 305 average time/residue: 0.5039 time to fit residues: 174.6657 Evaluate side-chains 307 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 94 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 72 SER Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 202 optimal weight: 0.0570 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 428 HIS 3 256 GLN 3 269 GLN 6 57 GLN 9 35 GLN A 92 ASN E 98 GLN F 87 ASN J 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098830 restraints weight = 22289.683| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.53 r_work: 0.2875 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17638 Z= 0.130 Angle : 0.495 10.328 23933 Z= 0.255 Chirality : 0.036 0.195 2829 Planarity : 0.004 0.056 3016 Dihedral : 3.973 27.152 2411 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.62 % Rotamer: Outliers : 2.02 % Allowed : 17.97 % Favored : 80.01 % 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: 2.54 (0.18), residues: 2271 helix: 2.16 (0.12), residues: 1736 sheet: None (None), residues: 0 loop : 0.17 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 91 TYR 0.036 0.002 TYR A 102 PHE 0.015 0.001 PHE 3 115 TRP 0.011 0.001 TRP 1 583 HIS 0.012 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00280 (17635) covalent geometry : angle 0.49443 (23931) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.93399 ( 2) hydrogen bonds : bond 0.04320 ( 1337) hydrogen bonds : angle 3.63180 ( 3933) metal coordination : bond 0.00131 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.4630 (OUTLIER) cc_final: 0.4017 (pm20) REVERT: 1 34 GLU cc_start: 0.5811 (tp30) cc_final: 0.4763 (pm20) REVERT: 1 224 LYS cc_start: 0.8522 (mtmm) cc_final: 0.7301 (pptt) REVERT: 1 339 GLU cc_start: 0.7101 (tp30) cc_final: 0.6877 (tp30) REVERT: 1 387 ARG cc_start: 0.8204 (mtp180) cc_final: 0.7628 (mtm-85) REVERT: 1 415 GLU cc_start: 0.8139 (tt0) cc_final: 0.7826 (tm-30) REVERT: 1 438 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8216 (tp-100) REVERT: 1 441 PHE cc_start: 0.7995 (m-80) cc_final: 0.7413 (m-80) REVERT: 1 452 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7519 (tm-30) REVERT: 1 501 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7916 (mm-30) REVERT: 3 98 VAL cc_start: 0.6530 (OUTLIER) cc_final: 0.6127 (t) REVERT: 5 112 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8504 (ptm-80) REVERT: 6 37 LYS cc_start: 0.8826 (tttp) cc_final: 0.8579 (tttm) REVERT: 9 1 MET cc_start: 0.3407 (tmt) cc_final: -0.1395 (ptp) REVERT: 9 9 LYS cc_start: 0.7087 (ttpt) cc_final: 0.6441 (ttpp) REVERT: 9 32 SER cc_start: 0.7764 (OUTLIER) cc_final: 0.7338 (p) REVERT: B 81 MET cc_start: 0.8996 (ttp) cc_final: 0.8573 (ttp) REVERT: B 115 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7719 (mm) REVERT: D 94 ASN cc_start: 0.7976 (m-40) cc_final: 0.7631 (m110) REVERT: D 119 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7391 (tm) REVERT: F 92 ASN cc_start: 0.8679 (t0) cc_final: 0.8324 (t0) REVERT: H 61 MET cc_start: 0.8039 (mmt) cc_final: 0.7573 (mtt) REVERT: H 81 MET cc_start: 0.8479 (ttp) cc_final: 0.8249 (ttp) REVERT: I 92 ASN cc_start: 0.8607 (t0) cc_final: 0.8394 (t0) REVERT: J 66 CYS cc_start: 0.8425 (m) cc_final: 0.7971 (m) REVERT: J 111 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: M 251 LEU cc_start: 0.9085 (tp) cc_final: 0.8865 (mt) outliers start: 36 outliers final: 26 residues processed: 306 average time/residue: 0.5093 time to fit residues: 176.6359 Evaluate side-chains 305 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 41 GLU Chi-restraints excluded: chain 1 residue 75 SER Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 499 GLU Chi-restraints excluded: chain 1 residue 500 LEU Chi-restraints excluded: chain 3 residue 98 VAL Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 287 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 5 residue 72 SER Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 100 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 8 LEU Chi-restraints excluded: chain 8 residue 67 SER Chi-restraints excluded: chain 8 residue 71 LYS Chi-restraints excluded: chain 9 residue 32 SER Chi-restraints excluded: chain 9 residue 96 SER Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain M residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 185 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 178 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 48 optimal weight: 0.0050 chunk 177 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 428 HIS 3 256 GLN 3 269 GLN 6 57 GLN 9 35 GLN A 92 ASN E 98 GLN F 87 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.099123 restraints weight = 22577.587| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.59 r_work: 0.2862 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17638 Z= 0.131 Angle : 0.504 10.319 23933 Z= 0.258 Chirality : 0.036 0.179 2829 Planarity : 0.004 0.056 3016 Dihedral : 3.963 26.941 2411 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 1.85 % Allowed : 18.87 % Favored : 79.28 % 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: 2.58 (0.18), residues: 2271 helix: 2.18 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : 0.20 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 91 TYR 0.042 0.002 TYR A 102 PHE 0.025 0.001 PHE 9 29 TRP 0.011 0.001 TRP 1 583 HIS 0.009 0.001 HIS 1 428 Details of bonding type rmsd covalent geometry : bond 0.00284 (17635) covalent geometry : angle 0.50376 (23931) SS BOND : bond 0.00150 ( 1) SS BOND : angle 1.59500 ( 2) hydrogen bonds : bond 0.04327 ( 1337) hydrogen bonds : angle 3.62674 ( 3933) metal coordination : bond 0.00130 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7553.68 seconds wall clock time: 128 minutes 55.92 seconds (7735.92 seconds total)