Starting phenix.real_space_refine on Fri Feb 6 21:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q80_52879/02_2026/9q80_52879.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q80_52879/02_2026/9q80_52879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q80_52879/02_2026/9q80_52879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q80_52879/02_2026/9q80_52879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q80_52879/02_2026/9q80_52879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q80_52879/02_2026/9q80_52879.map" } resolution = 3.39 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 298 5.49 5 S 72 5.16 5 C 16676 2.51 5 N 4924 2.21 5 O 5798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27768 Number of models: 1 Model: "" Number of chains: 14 Chain: "K" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4173 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 29, 'TRANS': 539} Chain breaks: 1 Unresolved non-hydrogen bonds: 433 Unresolved non-hydrogen angles: 515 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 17, 'GLN:plan1': 4, 'GLU:plan': 13, 'ASP:plan': 14, 'PHE:plan': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASP%COO:plan': 1} Unresolved non-hydrogen planarities: 257 Chain: "L" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3829 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 26, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 405 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 356 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 14, 'ASN:plan1': 2, 'GLN:plan1': 5, 'PHE:plan': 6, 'ASP:plan': 9, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 216 Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 754 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 793 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "M" Number of atoms: 3662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3662 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 27, 'TRANS': 465} Chain breaks: 1 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 8, 'PHE:plan': 10, 'TYR:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 8, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 214 Chain: "N" Number of atoms: 3990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3990 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 11, 'GLN:plan1': 5, 'TYR:plan': 2, 'ARG:plan': 5, 'HIS:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 143 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "I" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3075 Classifications: {'DNA': 151} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3053 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Time building chain proxies: 6.05, per 1000 atoms: 0.22 Number of scatterers: 27768 At special positions: 0 Unit cell: (107.944, 149.144, 223.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 298 15.00 O 5798 8.00 N 4924 7.00 C 16676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 970.6 milliseconds 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5460 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 24 sheets defined 45.0% alpha, 9.7% beta 111 base pairs and 216 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'K' and resid 45 through 50 Processing helix chain 'K' and resid 58 through 78 Processing helix chain 'K' and resid 113 through 121 removed outlier: 3.577A pdb=" N LEU K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 142 through 156 Processing helix chain 'K' and resid 179 through 197 removed outlier: 3.533A pdb=" N GLY K 197 " --> pdb=" O LEU K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 250 removed outlier: 3.934A pdb=" N LEU K 242 " --> pdb=" O LYS K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 330 through 338 removed outlier: 3.731A pdb=" N LYS K 338 " --> pdb=" O THR K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 393 removed outlier: 3.749A pdb=" N LEU K 381 " --> pdb=" O GLY K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 455 through 469 removed outlier: 3.624A pdb=" N LEU K 469 " --> pdb=" O ILE K 465 " (cutoff:3.500A) Processing helix chain 'K' and resid 484 through 495 Processing helix chain 'K' and resid 513 through 519 Processing helix chain 'K' and resid 520 through 530 Processing helix chain 'K' and resid 563 through 571 removed outlier: 5.011A pdb=" N SER K 569 " --> pdb=" O LYS K 565 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS K 570 " --> pdb=" O THR K 566 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 575 Processing helix chain 'K' and resid 577 through 589 Processing helix chain 'K' and resid 595 through 607 Processing helix chain 'L' and resid 17 through 22 removed outlier: 3.677A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN L 22 " --> pdb=" O PHE L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 29 through 47 Processing helix chain 'L' and resid 87 through 96 Processing helix chain 'L' and resid 106 through 122 Processing helix chain 'L' and resid 143 through 146 removed outlier: 3.831A pdb=" N GLN L 146 " --> pdb=" O SER L 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 143 through 146' Processing helix chain 'L' and resid 147 through 157 Processing helix chain 'L' and resid 198 through 211 Processing helix chain 'L' and resid 212 through 217 Processing helix chain 'L' and resid 218 through 222 removed outlier: 3.801A pdb=" N ASP L 222 " --> pdb=" O ASP L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 231 removed outlier: 3.707A pdb=" N LEU L 231 " --> pdb=" O PHE L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 241 Processing helix chain 'L' and resid 325 through 330 Processing helix chain 'L' and resid 352 through 356 Processing helix chain 'L' and resid 370 through 387 Processing helix chain 'L' and resid 441 through 445 removed outlier: 3.569A pdb=" N ALA L 445 " --> pdb=" O LYS L 442 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 461 Processing helix chain 'L' and resid 484 through 500 removed outlier: 4.149A pdb=" N GLN L 488 " --> pdb=" O ASN L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 509 through 516 removed outlier: 3.504A pdb=" N TRP L 513 " --> pdb=" O GLN L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 524 removed outlier: 3.588A pdb=" N THR L 523 " --> pdb=" O PRO L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 537 removed outlier: 3.749A pdb=" N LEU L 536 " --> pdb=" O LYS L 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.351A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.544A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.970A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.878A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.010A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.298A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'M' and resid 45 through 50 removed outlier: 3.663A pdb=" N PHE M 49 " --> pdb=" O LYS M 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU M 50 " --> pdb=" O ALA M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 78 Processing helix chain 'M' and resid 112 through 120 removed outlier: 3.613A pdb=" N ASP M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 135 removed outlier: 3.604A pdb=" N GLY M 127 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP M 133 " --> pdb=" O LYS M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 157 removed outlier: 3.832A pdb=" N VAL M 157 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 196 removed outlier: 4.002A pdb=" N LYS M 189 " --> pdb=" O ARG M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 251 Processing helix chain 'M' and resid 330 through 338 removed outlier: 3.863A pdb=" N LYS M 338 " --> pdb=" O THR M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 393 removed outlier: 3.686A pdb=" N LEU M 381 " --> pdb=" O GLY M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 455 through 468 Processing helix chain 'M' and resid 480 through 494 Processing helix chain 'M' and resid 510 through 519 Processing helix chain 'M' and resid 520 through 528 Processing helix chain 'N' and resid 29 through 47 removed outlier: 3.770A pdb=" N GLN N 33 " --> pdb=" O SER N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 97 Processing helix chain 'N' and resid 106 through 120 Processing helix chain 'N' and resid 146 through 155 Processing helix chain 'N' and resid 200 through 215 removed outlier: 3.684A pdb=" N GLY N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU N 205 " --> pdb=" O GLN N 201 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU N 206 " --> pdb=" O LYS N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 216 through 223 removed outlier: 3.859A pdb=" N LEU N 221 " --> pdb=" O GLU N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 233 removed outlier: 3.657A pdb=" N LEU N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG N 232 " --> pdb=" O SER N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 238 removed outlier: 3.533A pdb=" N LYS N 238 " --> pdb=" O CYS N 235 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 352 through 356 Processing helix chain 'N' and resid 370 through 387 Processing helix chain 'N' and resid 447 through 461 Processing helix chain 'N' and resid 484 through 500 Processing helix chain 'N' and resid 509 through 515 Processing helix chain 'N' and resid 519 through 537 removed outlier: 4.555A pdb=" N ILE N 528 " --> pdb=" O THR N 524 " (cutoff:3.500A) Proline residue: N 529 - end of helix Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.127A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.610A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.736A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.615A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 102 through 104 removed outlier: 3.755A pdb=" N TYR K 103 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE K 87 " --> pdb=" O TYR K 103 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER K 37 " --> pdb=" O ARG K 165 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET K 167 " --> pdb=" O SER K 37 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE K 39 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE K 169 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU K 41 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 260 through 262 removed outlier: 3.704A pdb=" N PHE K 367 " --> pdb=" O TYR K 274 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL K 394 " --> pdb=" O PRO K 415 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG K 399 " --> pdb=" O LEU K 347 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU K 347 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 286 through 287 Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.802A pdb=" N ALA L 9 " --> pdb=" O HIS L 131 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU L 133 " --> pdb=" O ALA L 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 10 removed outlier: 6.802A pdb=" N ALA L 9 " --> pdb=" O HIS L 131 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU L 133 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER L 160 " --> pdb=" O ARG L 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 249 through 253 removed outlier: 7.683A pdb=" N VAL L 361 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL L 390 " --> pdb=" O PHE L 345 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE L 345 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE L 392 " --> pdb=" O LEU L 343 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL L 342 " --> pdb=" O ARG L 250 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR L 252 " --> pdb=" O VAL L 342 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLY L 344 " --> pdb=" O THR L 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.662A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.880A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.488A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.019A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'G' and resid 101 through 102 removed outlier: 6.901A pdb=" N THR G 101 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'M' and resid 82 through 85 removed outlier: 4.040A pdb=" N PHE M 169 " --> pdb=" O LEU M 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 261 through 262 removed outlier: 7.113A pdb=" N LYS M 262 " --> pdb=" O LEU M 347 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY M 349 " --> pdb=" O LYS M 262 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU M 347 " --> pdb=" O ARG M 399 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG M 399 " --> pdb=" O LEU M 347 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR M 369 " --> pdb=" O GLY M 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 296 through 297 removed outlier: 3.606A pdb=" N CYS N 296 " --> pdb=" O LYS M 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 318 through 319 Processing sheet with id=AB9, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.955A pdb=" N GLU N 53 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU N 12 " --> pdb=" O GLU N 53 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA N 9 " --> pdb=" O HIS N 131 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLU N 133 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL N 11 " --> pdb=" O GLU N 133 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE N 135 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS N 13 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG N 130 " --> pdb=" O SER N 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'N' and resid 57 through 59 Processing sheet with id=AC2, first strand: chain 'N' and resid 164 through 165 Processing sheet with id=AC3, first strand: chain 'N' and resid 247 through 253 removed outlier: 3.848A pdb=" N LEU N 257 " --> pdb=" O ILE N 253 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLN N 360 " --> pdb=" O GLN N 423 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN N 423 " --> pdb=" O GLN N 360 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU N 419 " --> pdb=" O VAL N 364 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA N 366 " --> pdb=" O GLU N 417 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N GLU N 417 " --> pdb=" O ALA N 366 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL N 390 " --> pdb=" O PHE N 345 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE N 345 " --> pdb=" O VAL N 390 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE N 392 " --> pdb=" O LEU N 343 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 247 through 253 removed outlier: 3.848A pdb=" N LEU N 257 " --> pdb=" O ILE N 253 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N GLN N 360 " --> pdb=" O GLN N 423 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN N 423 " --> pdb=" O GLN N 360 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU N 419 " --> pdb=" O VAL N 364 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA N 366 " --> pdb=" O GLU N 417 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N GLU N 417 " --> pdb=" O ALA N 366 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS N 418 " --> pdb=" O HIS N 411 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS N 411 " --> pdb=" O CYS N 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.224A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.544A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1000 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 286 hydrogen bonds 560 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 216 stacking parallelities Total time for adding SS restraints: 5.67 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8058 1.34 - 1.46: 8030 1.46 - 1.58: 12095 1.58 - 1.70: 595 1.70 - 1.82: 114 Bond restraints: 28892 Sorted by residual: bond pdb=" CD GLN K 68 " pdb=" OE1 GLN K 68 " ideal model delta sigma weight residual 1.231 1.281 -0.050 1.90e-02 2.77e+03 7.04e+00 bond pdb=" C LEU M 311 " pdb=" N LEU M 312 " ideal model delta sigma weight residual 1.333 1.369 -0.036 2.74e-02 1.33e+03 1.74e+00 bond pdb=" C3' DC I 121 " pdb=" O3' DC I 121 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" C3' DG J 72 " pdb=" O3' DG J 72 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C3' DA J 119 " pdb=" O3' DA J 119 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.58e+00 ... (remaining 28887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 39916 2.46 - 4.93: 519 4.93 - 7.39: 27 7.39 - 9.86: 4 9.86 - 12.32: 2 Bond angle restraints: 40468 Sorted by residual: angle pdb=" C LYS K 556 " pdb=" CA LYS K 556 " pdb=" CB LYS K 556 " ideal model delta sigma weight residual 116.54 111.62 4.92 1.15e+00 7.56e-01 1.83e+01 angle pdb=" C PRO K 532 " pdb=" N ASP K 533 " pdb=" CA ASP K 533 " ideal model delta sigma weight residual 120.90 126.86 -5.96 1.41e+00 5.03e-01 1.79e+01 angle pdb=" CB MET N 515 " pdb=" CG MET N 515 " pdb=" SD MET N 515 " ideal model delta sigma weight residual 112.70 125.02 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C SER K 139 " pdb=" CA SER K 139 " pdb=" CB SER K 139 " ideal model delta sigma weight residual 116.54 111.89 4.65 1.15e+00 7.56e-01 1.63e+01 angle pdb=" CB MET K 446 " pdb=" CG MET K 446 " pdb=" SD MET K 446 " ideal model delta sigma weight residual 112.70 123.37 -10.67 3.00e+00 1.11e-01 1.26e+01 ... (remaining 40463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 14783 34.58 - 69.16: 1842 69.16 - 103.75: 80 103.75 - 138.33: 2 138.33 - 172.91: 4 Dihedral angle restraints: 16711 sinusoidal: 8314 harmonic: 8397 Sorted by residual: dihedral pdb=" CA SER M 45 " pdb=" C SER M 45 " pdb=" N LYS M 46 " pdb=" CA LYS M 46 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA LYS M 100 " pdb=" C LYS M 100 " pdb=" N ASN M 101 " pdb=" CA ASN M 101 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DG J 72 " pdb=" C3' DG J 72 " pdb=" O3' DG J 72 " pdb=" P DG J 73 " ideal model delta sinusoidal sigma weight residual -140.00 32.91 -172.91 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 16708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3313 0.034 - 0.068: 1026 0.068 - 0.101: 266 0.101 - 0.135: 92 0.135 - 0.169: 11 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CB ILE K 67 " pdb=" CA ILE K 67 " pdb=" CG1 ILE K 67 " pdb=" CG2 ILE K 67 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CB ILE L 94 " pdb=" CA ILE L 94 " pdb=" CG1 ILE L 94 " pdb=" CG2 ILE L 94 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE K 102 " pdb=" N ILE K 102 " pdb=" C ILE K 102 " pdb=" CB ILE K 102 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 4705 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 142 " -0.047 2.00e-02 2.50e+03 1.95e-02 1.04e+01 pdb=" N9 DA I 142 " 0.013 2.00e-02 2.50e+03 pdb=" C8 DA I 142 " 0.016 2.00e-02 2.50e+03 pdb=" N7 DA I 142 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DA I 142 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DA I 142 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 142 " -0.029 2.00e-02 2.50e+03 pdb=" N1 DA I 142 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 142 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA I 142 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DA I 142 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 72 " 0.029 2.00e-02 2.50e+03 1.29e-02 4.55e+00 pdb=" N9 DA I 72 " -0.005 2.00e-02 2.50e+03 pdb=" C8 DA I 72 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DA I 72 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA I 72 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DA I 72 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 72 " 0.023 2.00e-02 2.50e+03 pdb=" N1 DA I 72 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 72 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 72 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 72 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO K 531 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO K 532 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO K 532 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 532 " -0.029 5.00e-02 4.00e+02 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 12801 2.96 - 3.44: 29358 3.44 - 3.93: 49972 3.93 - 4.41: 56146 4.41 - 4.90: 82180 Nonbonded interactions: 230457 Sorted by model distance: nonbonded pdb=" O4 DT I 5 " pdb=" N3 DC J 148 " model vdw 2.475 2.496 nonbonded pdb=" O5' DT J 146 " pdb=" O4' DT J 146 " model vdw 2.488 2.432 nonbonded pdb=" O5' DG I 66 " pdb=" O4' DG I 66 " model vdw 2.520 2.432 nonbonded pdb=" N GLU C 91 " pdb=" OE1 GLU C 91 " model vdw 2.523 3.120 nonbonded pdb=" O5' DG J 150 " pdb=" O4' DG J 150 " model vdw 2.535 2.432 ... (remaining 230452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 133)) selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 100) } ncs_group { reference = (chain 'C' and resid 13 through 116) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 27 through 122) selection = (chain 'H' and (resid 27 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 104 or (resid 105 and (name N or n \ ame CA or name C or name O or name CB )) or resid 106 through 121 or (resid 122 \ and (name N or name CA or name C or name O or name CB or name OXT)))) } ncs_group { reference = (chain 'K' and (resid 34 through 37 or (resid 38 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 49 or (resid 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 59 or (res \ id 60 and (name N or name CA or name C or name O or name CB )) or resid 61 throu \ gh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or r \ esid 88 through 91 or (resid 92 and (name N or name CA or name C or name O or na \ me CB )) or resid 93 or (resid 94 and (name N or name CA or name C or name O or \ name CB )) or resid 95 through 98 or (resid 99 through 100 and (name N or name C \ A or name C or name O or name CB )) or resid 101 through 102 or (resid 103 and ( \ name N or name CA or name C or name O or name CB )) or resid 104 through 117 or \ (resid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ through 120 or (resid 121 through 122 and (name N or name CA or name C or name \ O or name CB )) or resid 123 through 125 or (resid 126 and (name N or name CA or \ name C or name O or name CB )) or resid 127 through 129 or (resid 130 through 1 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 136 through \ 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) or r \ esid 141 through 147 or (resid 148 and (name N or name CA or name C or name O or \ name CB )) or resid 149 through 159 or (resid 160 through 161 and (name N or na \ me CA or name C or name O or name CB )) or resid 162 through 163 or (resid 164 a \ nd (name N or name CA or name C or name O or name CB )) or resid 165 through 184 \ or (resid 185 through 190 and (name N or name CA or name C or name O or name CB \ )) or resid 191 through 198 or (resid 199 and (name N or name CA or name C or n \ ame O or name CB )) or resid 200 through 205 or (resid 206 and (name N or name C \ A or name C or name O or name CB )) or resid 207 through 210 or (resid 211 throu \ gh 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thr \ ough 215 or (resid 216 and (name N or name CA or name C or name O or name CB )) \ or resid 217 through 222 or resid 231 through 239 or (resid 240 through 241 and \ (name N or name CA or name C or name O or name CB )) or resid 242 through 243 or \ (resid 244 through 245 and (name N or name CA or name C or name O or name CB )) \ or resid 246 through 293 or (resid 294 and (name N or name CA or name C or name \ O or name CB )) or resid 295 through 298 or (resid 299 and (name N or name CA o \ r name C or name O or name CB )) or resid 300 through 331 or (resid 332 and (nam \ e N or name CA or name C or name O or name CB )) or resid 333 through 362 or (re \ sid 363 and (name N or name CA or name C or name O or name CB )) or resid 364 th \ rough 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) \ or resid 394 through 399 or (resid 400 and (name N or name CA or name C or name \ O or name CB )) or resid 401 through 451 or (resid 452 through 454 and (name N \ or name CA or name C or name O or name CB )) or resid 455 through 494 or (resid \ 495 and (name N or name CA or name C or name O or name CB )) or resid 496 throug \ h 509 or (resid 510 and (name N or name CA or name C or name O or name CB )) or \ resid 511 through 515 or (resid 516 through 517 and (name N or name CA or name C \ or name O or name CB )) or resid 518 through 523 or (resid 524 through 527 and \ (name N or name CA or name C or name O or name CB )) or resid 528 through 533 or \ (resid 534 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 34 or (resid 35 and (name N or name CA or name C or name O \ or name CB )) or resid 36 or (resid 37 through 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 51 or (resid 52 and (name N or n \ ame CA or name C or name O or name CB )) or resid 53 or (resid 54 through 57 and \ (name N or name CA or name C or name O or name CB )) or resid 58 through 64 or \ (resid 65 and (name N or name CA or name C or name O or name CB )) or resid 66 t \ hrough 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) \ or resid 80 or (resid 81 and (name N or name CA or name C or name O or name CB ) \ ) or resid 82 through 99 or (resid 100 and (name N or name CA or name C or name \ O or name CB )) or resid 101 through 105 or (resid 106 and (name N or name CA or \ name C or name O or name CB )) or resid 107 through 131 or (resid 132 through 1 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 136 through \ 142 or (resid 143 and (name N or name CA or name C or name O or name CB )) or r \ esid 144 through 149 or (resid 150 through 151 and (name N or name CA or name C \ or name O or name CB )) or resid 152 through 155 or (resid 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 through 162 or (resid 163 t \ hrough 164 and (name N or name CA or name C or name O or name CB )) or resid 165 \ through 166 or (resid 167 and (name N or name CA or name C or name O or name CB \ )) or resid 168 through 188 or (resid 189 through 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 193 or (resid 194 through 1 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 196 through \ 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or r \ esid 215 through 231 or (resid 232 and (name N or name CA or name C or name O or \ name CB )) or resid 233 through 236 or (resid 237 through 238 and (name N or na \ me CA or name C or name O or name CB )) or resid 239 through 240 or (resid 241 a \ nd (name N or name CA or name C or name O or name CB )) or resid 242 through 244 \ or (resid 245 and (name N or name CA or name C or name O or name CB )) or resid \ 246 or (resid 247 through 248 and (name N or name CA or name C or name O or nam \ e CB )) or resid 249 through 251 or (resid 252 through 255 and (name N or name C \ A or name C or name O or name CB )) or resid 256 through 259 or (resid 260 and ( \ name N or name CA or name C or name O or name CB )) or resid 261 through 278 or \ (resid 279 through 282 and (name N or name CA or name C or name O or name CB )) \ or resid 283 through 302 or (resid 303 and (name N or name CA or name C or name \ O or name CB )) or resid 304 through 306 or resid 314 through 317 or (resid 318 \ and (name N or name CA or name C or name O or name CB )) or resid 319 through 32 \ 3 or (resid 324 and (name N or name CA or name C or name O or name CB )) or resi \ d 325 through 330 or (resid 331 through 332 and (name N or name CA or name C or \ name O or name CB )) or resid 333 through 334 or (resid 335 and (name N or name \ CA or name C or name O or name CB )) or resid 336 through 384 or (resid 385 and \ (name N or name CA or name C or name O or name CB )) or resid 386 through 391 or \ (resid 392 through 393 and (name N or name CA or name C or name O or name CB )) \ or resid 394 through 398 or (resid 399 through 400 and (name N or name CA or na \ me C or name O or name CB )) or resid 401 through 403 or (resid 404 and (name N \ or name CA or name C or name O or name CB )) or resid 405 through 419 or (resid \ 420 and (name N or name CA or name C or name O or name CB )) or resid 421 or (re \ sid 422 and (name N or name CA or name C or name O or name CB )) or resid 423 or \ (resid 424 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 5 through 431 or (resid 432 and (name N or name CA or name C or name O or name C \ B )) or resid 433 through 440 or (resid 441 and (name N or name CA or name C or \ name O or name CB )) or resid 442 through 444 or (resid 445 and (name N or name \ CA or name C or name O or name CB )) or resid 446 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 451 through 460 or \ (resid 461 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 2 through 473 or (resid 474 and (name N or name CA or name C or name O or name C \ B )) or resid 475 through 478 or (resid 479 and (name N or name CA or name C or \ name O or name CB )) or resid 480 through 500 or (resid 501 and (name N or name \ CA or name C or name O or name CB )) or resid 502 through 516 or (resid 517 and \ (name N or name CA or name C or name O or name CB )) or resid 518 through 534)) } ncs_group { reference = (chain 'L' and (resid 6 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 71 or (resid 72 throug \ h 74 and (name N or name CA or name C or name O or name CB )) or resid 75 throug \ h 84 or (resid 85 and (name N or name CA or name C or name O or name CB )) or re \ sid 86 through 88 or (resid 89 through 90 and (name N or name CA or name C or na \ me O or name CB )) or resid 91 through 92 or (resid 93 and (name N or name CA or \ name C or name O or name CB )) or resid 94 through 103 or (resid 104 through 10 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 106 through \ 147 or (resid 148 and (name N or name CA or name C or name O or name CB )) or re \ sid 149 through 151 or (resid 152 and (name N or name CA or name C or name O or \ name CB )) or resid 153 through 196 or (resid 197 through 200 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 or (resid 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 through 209 or (resid 21 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 211 or (resi \ d 212 and (name N or name CA or name C or name O or name CB )) or resid 213 thro \ ugh 233 or (resid 234 and (name N or name CA or name C or name O or name CB )) o \ r resid 235 through 252 or (resid 253 and (name N or name CA or name C or name O \ or name CB )) or resid 254 or (resid 255 through 256 and (name N or name CA or \ name C or name O or name CB )) or resid 257 through 259 or (resid 260 and (name \ N or name CA or name C or name O or name CB )) or resid 261 through 268 or (resi \ d 269 and (name N or name CA or name C or name O or name CB )) or resid 270 thro \ ugh 286 or (resid 287 and (name N or name CA or name C or name O or name CB )) o \ r resid 288 through 300 or (resid 301 and (name N or name CA or name C or name O \ or name CB )) or resid 302 through 309 or (resid 310 and (name N or name CA or \ name C or name O or name CB )) or resid 311 through 335 or (resid 336 and (name \ N or name CA or name C or name O or name CB )) or resid 337 through 359 or (resi \ d 360 and (name N or name CA or name C or name O or name CB )) or resid 361 thro \ ugh 387 or (resid 388 through 389 and (name N or name CA or name C or name O or \ name CB )) or resid 390 through 397 or (resid 398 and (name N or name CA or name \ C or name O or name CB )) or resid 399 through 422 or (resid 423 and (name N or \ name CA or name C or name O or name CB )) or resid 424 through 426 or (resid 42 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 428 through \ 439 or (resid 440 and (name N or name CA or name C or name O or name CB )) or re \ sid 441 through 443 or (resid 444 through 445 and (name N or name CA or name C o \ r name O or name CB )) or resid 446 through 447 or (resid 448 through 449 and (n \ ame N or name CA or name C or name O or name CB )) or resid 450 or (resid 451 an \ d (name N or name CA or name C or name O or name CB )) or resid 452 through 478 \ or (resid 479 and (name N or name CA or name C or name O or name CB )) or resid \ 480 through 543)) selection = (chain 'N' and (resid 6 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 34 or (resid 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 43 or (resid 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 48 or (re \ sid 49 and (name N or name CA or name C or name O or name CB )) or resid 50 thro \ ugh 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or \ resid 67 through 98 or (resid 99 and (name N or name CA or name C or name O or n \ ame CB )) or resid 100 through 101 or (resid 102 and (name N or name CA or name \ C or name O or name CB )) or resid 103 through 106 or (resid 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 128 or (resid 129 \ and (name N or name CA or name C or name O or name CB )) or resid 130 through 1 \ 36 or (resid 137 and (name N or name CA or name C or name O or name CB )) or res \ id 138 through 154 or (resid 155 and (name N or name CA or name C or name O or n \ ame CB )) or resid 156 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 166 or (resid 167 and (name N or \ name CA or name C or name O or name CB )) or resid 168 through 184 or (resid 185 \ and (name N or name CA or name C or name O or name CB )) or resid 186 through 1 \ 91 or (resid 192 and (name N or name CA or name C or name O or name CB )) or res \ id 193 through 197 or (resid 198 through 200 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 208 or (resid 209 through 210 and (na \ me N or name CA or name C or name O or name CB )) or resid 211 through 218 or (r \ esid 219 and (name N or name CA or name C or name O or name CB )) or resid 220 t \ hrough 228 or (resid 229 and (name N or name CA or name C or name O or name CB ) \ ) or resid 230 through 232 or (resid 233 through 234 and (name N or name CA or n \ ame C or name O or name CB )) or resid 235 through 237 or (resid 238 through 239 \ and (name N or name CA or name C or name O or name CB )) or resid 240 or (resid \ 241 through 242 and (name N or name CA or name C or name O or name CB )) or res \ id 243 through 249 or (resid 250 and (name N or name CA or name C or name O or n \ ame CB )) or resid 251 through 270 or (resid 271 and (name N or name CA or name \ C or name O or name CB )) or resid 272 or (resid 273 through 274 and (name N or \ name CA or name C or name O or name CB )) or resid 275 or (resid 276 and (name N \ or name CA or name C or name O or name CB )) or resid 277 through 281 or (resid \ 282 and (name N or name CA or name C or name O or name CB )) or resid 283 or (r \ esid 284 through 287 and (name N or name CA or name C or name O or name CB )) or \ resid 288 through 302 or (resid 303 through 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 or (resid 306 through 308 and (name N or \ name CA or name C or name O or name CB )) or resid 309 through 325 or (resid 326 \ and (name N or name CA or name C or name O or name CB )) or resid 327 through 3 \ 28 or (resid 329 through 336 and (name N or name CA or name C or name O or name \ CB )) or resid 337 or (resid 338 and (name N or name CA or name C or name O or n \ ame CB )) or resid 339 through 351 or (resid 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 367 or (resid 368 through 369 and \ (name N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 \ through 374 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 75 through 381 or (resid 382 through 383 and (name N or name CA or name C or nam \ e O or name CB )) or resid 384 or (resid 385 through 386 and (name N or name CA \ or name C or name O or name CB )) or resid 387 through 388 or (resid 389 and (na \ me N or name CA or name C or name O or name CB )) or resid 390 through 414 or (r \ esid 415 and (name N or name CA or name C or name O or name CB )) or resid 416 t \ hrough 428 or (resid 429 and (name N or name CA or name C or name O or name CB ) \ ) or resid 430 through 431 or (resid 432 and (name N or name CA or name C or nam \ e O or name CB )) or resid 433 or (resid 434 and (name N or name CA or name C or \ name O or name CB )) or resid 435 through 464 or (resid 465 through 469 and (na \ me N or name CA or name C or name O or name CB )) or resid 470 through 471 or (r \ esid 472 through 474 and (name N or name CA or name C or name O or name CB )) or \ resid 475 through 488 or (resid 489 and (name N or name CA or name C or name O \ or name CB )) or resid 490 through 520 or (resid 521 and (name N or name CA or n \ ame C or name O or name CB )) or resid 522 through 524 or (resid 525 and (name N \ or name CA or name C or name O or name CB )) or resid 526 through 527 or (resid \ 528 and (name N or name CA or name C or name O or name CB )) or resid 529 or (r \ esid 530 and (name N or name CA or name C or name O or name CB )) or resid 531 t \ hrough 533 or (resid 534 and (name N or name CA or name C or name O or name CB ) \ ) or resid 535 through 536 or (resid 537 and (name N or name CA or name C or nam \ e O or name CB )) or resid 538 through 540 or (resid 541 through 543 and (name N \ or name CA or name C or name O or name CB )))) } 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: 8.870 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.240 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28892 Z= 0.183 Angle : 0.636 12.324 40468 Z= 0.365 Chirality : 0.037 0.169 4708 Planarity : 0.004 0.053 4164 Dihedral : 24.343 172.912 11251 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.16 % Favored : 89.53 % Rotamer: Outliers : 1.14 % Allowed : 32.41 % Favored : 66.45 % 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: -0.91 (0.16), residues: 2845 helix: 1.33 (0.15), residues: 1192 sheet: -1.32 (0.30), residues: 298 loop : -2.33 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 353 TYR 0.024 0.001 TYR M 88 PHE 0.016 0.001 PHE K 436 TRP 0.009 0.001 TRP K 148 HIS 0.006 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00372 (28892) covalent geometry : angle 0.63584 (40468) hydrogen bonds : bond 0.11782 ( 1274) hydrogen bonds : angle 5.92500 ( 3437) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 477 PHE cc_start: 0.0430 (OUTLIER) cc_final: -0.1023 (t80) REVERT: E 73 GLU cc_start: 0.9120 (tt0) cc_final: 0.8849 (tt0) REVERT: F 78 ARG cc_start: 0.9458 (OUTLIER) cc_final: 0.8759 (ttp-110) REVERT: G 61 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8678 (mt-10) REVERT: N 477 PHE cc_start: 0.0376 (OUTLIER) cc_final: -0.0835 (m-80) REVERT: B 74 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8870 (mm-30) outliers start: 25 outliers final: 17 residues processed: 143 average time/residue: 0.1595 time to fit residues: 39.2312 Evaluate side-chains 134 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 522 VAL Chi-restraints excluded: chain B residue 74 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS N 511 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.116437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.072515 restraints weight = 125438.476| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 7.73 r_work: 0.3039 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28892 Z= 0.189 Angle : 0.591 7.857 40468 Z= 0.329 Chirality : 0.039 0.154 4708 Planarity : 0.004 0.052 4164 Dihedral : 25.461 174.274 6368 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.69 % Favored : 89.00 % Rotamer: Outliers : 4.28 % Allowed : 29.77 % Favored : 65.95 % 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: -0.65 (0.16), residues: 2845 helix: 1.67 (0.15), residues: 1206 sheet: -1.21 (0.31), residues: 282 loop : -2.36 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 353 TYR 0.015 0.001 TYR M 88 PHE 0.015 0.001 PHE K 436 TRP 0.007 0.001 TRP N 513 HIS 0.005 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00415 (28892) covalent geometry : angle 0.59050 (40468) hydrogen bonds : bond 0.04986 ( 1274) hydrogen bonds : angle 4.71252 ( 3437) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 116 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 76 ILE cc_start: 0.5682 (OUTLIER) cc_final: 0.5407 (tt) REVERT: K 250 GLU cc_start: 0.4189 (OUTLIER) cc_final: 0.3608 (mp0) REVERT: K 598 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8357 (tm-30) REVERT: L 360 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.5035 (pp30) REVERT: L 477 PHE cc_start: -0.1434 (OUTLIER) cc_final: -0.2734 (t80) REVERT: M 168 LEU cc_start: -0.0084 (OUTLIER) cc_final: -0.0690 (mp) REVERT: N 477 PHE cc_start: -0.1373 (OUTLIER) cc_final: -0.2451 (m-80) REVERT: N 515 MET cc_start: 0.1134 (mmm) cc_final: 0.0808 (mmm) outliers start: 94 outliers final: 38 residues processed: 205 average time/residue: 0.1636 time to fit residues: 56.7114 Evaluate side-chains 155 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 556 LYS Chi-restraints excluded: chain K residue 598 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 168 LEU Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 455 THR Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 497 ARG Chi-restraints excluded: chain N residue 511 HIS Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 282 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 260 optimal weight: 0.4980 chunk 203 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 264 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS N 131 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.116826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073676 restraints weight = 123805.885| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 7.38 r_work: 0.3051 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28892 Z= 0.166 Angle : 0.575 7.733 40468 Z= 0.319 Chirality : 0.038 0.163 4708 Planarity : 0.004 0.058 4164 Dihedral : 25.529 173.467 6350 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.02 % Favored : 89.67 % Rotamer: Outliers : 4.10 % Allowed : 29.54 % Favored : 66.36 % 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: -0.59 (0.16), residues: 2845 helix: 1.77 (0.15), residues: 1196 sheet: -1.23 (0.32), residues: 284 loop : -2.33 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 353 TYR 0.020 0.001 TYR N 395 PHE 0.016 0.001 PHE K 436 TRP 0.006 0.001 TRP K 148 HIS 0.008 0.001 HIS N 511 Details of bonding type rmsd covalent geometry : bond 0.00363 (28892) covalent geometry : angle 0.57527 (40468) hydrogen bonds : bond 0.04448 ( 1274) hydrogen bonds : angle 4.53606 ( 3437) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 116 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 250 GLU cc_start: 0.4190 (OUTLIER) cc_final: 0.3568 (mp0) REVERT: K 446 MET cc_start: 0.6465 (mmm) cc_final: 0.6178 (mmt) REVERT: K 598 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: L 360 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.5015 (pp30) REVERT: E 73 GLU cc_start: 0.8951 (tt0) cc_final: 0.8714 (tt0) REVERT: M 167 MET cc_start: 0.1436 (mmm) cc_final: 0.0559 (mtp) REVERT: N 477 PHE cc_start: -0.1358 (OUTLIER) cc_final: -0.2151 (m-80) outliers start: 90 outliers final: 50 residues processed: 201 average time/residue: 0.1512 time to fit residues: 51.2065 Evaluate side-chains 160 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 556 LYS Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 598 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 462 MET Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 412 ILE Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 497 ARG Chi-restraints excluded: chain N residue 511 HIS Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 522 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 293 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 219 optimal weight: 7.9990 chunk 214 optimal weight: 30.0000 chunk 199 optimal weight: 0.5980 chunk 91 optimal weight: 40.0000 chunk 86 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.070238 restraints weight = 124198.727| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 6.75 r_work: 0.2997 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 28892 Z= 0.325 Angle : 0.667 8.556 40468 Z= 0.368 Chirality : 0.043 0.196 4708 Planarity : 0.005 0.057 4164 Dihedral : 25.780 176.381 6348 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.49 % Favored : 88.19 % Rotamer: Outliers : 4.78 % Allowed : 29.18 % Favored : 66.04 % 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: -0.77 (0.16), residues: 2845 helix: 1.58 (0.15), residues: 1193 sheet: -1.24 (0.32), residues: 279 loop : -2.39 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 353 TYR 0.035 0.002 TYR H 80 PHE 0.020 0.001 PHE K 436 TRP 0.006 0.001 TRP L 513 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00731 (28892) covalent geometry : angle 0.66710 (40468) hydrogen bonds : bond 0.05583 ( 1274) hydrogen bonds : angle 4.79540 ( 3437) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 106 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 250 GLU cc_start: 0.4359 (OUTLIER) cc_final: 0.3905 (mm-30) REVERT: K 446 MET cc_start: 0.6454 (mmm) cc_final: 0.6149 (mmt) REVERT: K 598 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: L 142 PHE cc_start: 0.3176 (OUTLIER) cc_final: 0.1924 (m-10) REVERT: L 477 PHE cc_start: -0.1393 (OUTLIER) cc_final: -0.2574 (t80) REVERT: E 52 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8477 (mtm180) REVERT: N 407 VAL cc_start: -0.1155 (OUTLIER) cc_final: -0.1396 (p) REVERT: N 477 PHE cc_start: -0.0907 (OUTLIER) cc_final: -0.1632 (m-80) REVERT: N 513 TRP cc_start: 0.4550 (OUTLIER) cc_final: 0.4269 (t60) REVERT: A 125 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8637 (mp10) outliers start: 105 outliers final: 67 residues processed: 209 average time/residue: 0.1553 time to fit residues: 54.0123 Evaluate side-chains 177 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 101 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 556 LYS Chi-restraints excluded: chain K residue 572 THR Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain K residue 598 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 291 GLU Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 507 THR Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 381 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 412 ILE Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 497 ARG Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 522 VAL Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 285 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 44 GLN ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 GLN N 120 HIS N 298 ASN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.114367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.069670 restraints weight = 122841.784| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 6.40 r_work: 0.2985 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 28892 Z= 0.369 Angle : 0.699 9.727 40468 Z= 0.385 Chirality : 0.044 0.192 4708 Planarity : 0.005 0.060 4164 Dihedral : 25.993 177.686 6348 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 11.67 % Favored : 88.01 % Rotamer: Outliers : 5.55 % Allowed : 28.68 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2845 helix: 1.37 (0.15), residues: 1193 sheet: -1.51 (0.31), residues: 292 loop : -2.43 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.021 0.002 TYR H 80 PHE 0.023 0.001 PHE K 436 TRP 0.006 0.001 TRP N 513 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00830 (28892) covalent geometry : angle 0.69886 (40468) hydrogen bonds : bond 0.05722 ( 1274) hydrogen bonds : angle 4.92974 ( 3437) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 107 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 154 PHE cc_start: 0.0783 (OUTLIER) cc_final: 0.0061 (m-80) REVERT: K 250 GLU cc_start: 0.4549 (OUTLIER) cc_final: 0.4126 (tp30) REVERT: K 446 MET cc_start: 0.6278 (mmm) cc_final: 0.6007 (mmt) REVERT: L 142 PHE cc_start: 0.3138 (OUTLIER) cc_final: 0.2098 (m-10) REVERT: L 477 PHE cc_start: -0.0888 (OUTLIER) cc_final: -0.2664 (t80) REVERT: E 52 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8561 (mtm-85) REVERT: M 203 MET cc_start: -0.4904 (mtt) cc_final: -0.5203 (mtp) REVERT: N 407 VAL cc_start: -0.0959 (OUTLIER) cc_final: -0.1186 (p) REVERT: N 477 PHE cc_start: -0.0710 (OUTLIER) cc_final: -0.1530 (m-80) REVERT: N 513 TRP cc_start: 0.4436 (OUTLIER) cc_final: 0.4166 (t60) outliers start: 122 outliers final: 83 residues processed: 225 average time/residue: 0.1595 time to fit residues: 60.9008 Evaluate side-chains 193 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 102 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain K residue 556 LYS Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 142 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 275 THR Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 361 VAL Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 269 ILE Chi-restraints excluded: chain M residue 291 GLU Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 455 THR Chi-restraints excluded: chain M residue 462 MET Chi-restraints excluded: chain M residue 504 VAL Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 134 ILE Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 381 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 412 ILE Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 497 ARG Chi-restraints excluded: chain N residue 511 HIS Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 522 VAL Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 0.6980 chunk 91 optimal weight: 30.0000 chunk 261 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 89 optimal weight: 30.0000 chunk 299 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN M 52 GLN N 120 HIS N 509 GLN A 108 ASN A 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.117044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.073627 restraints weight = 122549.605| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 7.72 r_work: 0.3072 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28892 Z= 0.143 Angle : 0.583 10.675 40468 Z= 0.323 Chirality : 0.038 0.152 4708 Planarity : 0.004 0.060 4164 Dihedral : 25.726 173.761 6348 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.26 % Favored : 89.42 % Rotamer: Outliers : 3.10 % Allowed : 30.91 % Favored : 66.00 % 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: -0.70 (0.16), residues: 2845 helix: 1.66 (0.15), residues: 1201 sheet: -1.52 (0.31), residues: 291 loop : -2.33 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.015 0.001 TYR M 88 PHE 0.017 0.001 PHE K 436 TRP 0.007 0.001 TRP K 148 HIS 0.006 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00308 (28892) covalent geometry : angle 0.58314 (40468) hydrogen bonds : bond 0.04247 ( 1274) hydrogen bonds : angle 4.39774 ( 3437) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 121 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 154 PHE cc_start: 0.1116 (OUTLIER) cc_final: 0.0382 (m-80) REVERT: K 250 GLU cc_start: 0.4286 (OUTLIER) cc_final: 0.3787 (mm-30) REVERT: K 446 MET cc_start: 0.6227 (mmm) cc_final: 0.5911 (mmt) REVERT: L 477 PHE cc_start: -0.0643 (OUTLIER) cc_final: -0.2259 (t80) REVERT: E 73 GLU cc_start: 0.8876 (tt0) cc_final: 0.8624 (tt0) REVERT: M 203 MET cc_start: -0.4744 (mtt) cc_final: -0.5169 (mtp) REVERT: N 407 VAL cc_start: -0.0964 (OUTLIER) cc_final: -0.1193 (p) REVERT: N 477 PHE cc_start: -0.0846 (OUTLIER) cc_final: -0.1768 (m-80) REVERT: N 513 TRP cc_start: 0.4484 (OUTLIER) cc_final: 0.4190 (t60) REVERT: A 108 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8971 (t0) outliers start: 68 outliers final: 37 residues processed: 185 average time/residue: 0.1618 time to fit residues: 51.1631 Evaluate side-chains 156 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 275 THR Chi-restraints excluded: chain L residue 427 MET Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 291 GLU Chi-restraints excluded: chain M residue 455 THR Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 412 ILE Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 497 ARG Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 20.0000 chunk 112 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 1 optimal weight: 40.0000 chunk 157 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 156 optimal weight: 0.0270 overall best weight: 1.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.116418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.072507 restraints weight = 123462.445| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 6.57 r_work: 0.3052 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28892 Z= 0.161 Angle : 0.581 9.684 40468 Z= 0.320 Chirality : 0.038 0.151 4708 Planarity : 0.004 0.058 4164 Dihedral : 25.634 174.179 6344 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.30 % Favored : 89.42 % Rotamer: Outliers : 3.05 % Allowed : 30.91 % Favored : 66.04 % 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: -0.67 (0.16), residues: 2845 helix: 1.66 (0.15), residues: 1208 sheet: -1.47 (0.31), residues: 296 loop : -2.32 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.017 0.001 TYR H 80 PHE 0.020 0.001 PHE K 436 TRP 0.005 0.001 TRP N 513 HIS 0.006 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00355 (28892) covalent geometry : angle 0.58063 (40468) hydrogen bonds : bond 0.04301 ( 1274) hydrogen bonds : angle 4.37123 ( 3437) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 110 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 154 PHE cc_start: 0.0544 (OUTLIER) cc_final: -0.0127 (m-80) REVERT: K 250 GLU cc_start: 0.4206 (OUTLIER) cc_final: 0.3707 (mm-30) REVERT: K 446 MET cc_start: 0.6339 (mmm) cc_final: 0.6033 (mmt) REVERT: L 477 PHE cc_start: -0.1561 (OUTLIER) cc_final: -0.2969 (t80) REVERT: F 84 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7874 (mmt) REVERT: M 203 MET cc_start: -0.4915 (mtt) cc_final: -0.5207 (mtp) REVERT: N 407 VAL cc_start: -0.0944 (OUTLIER) cc_final: -0.1194 (p) REVERT: N 477 PHE cc_start: -0.0985 (OUTLIER) cc_final: -0.1901 (m-80) REVERT: N 513 TRP cc_start: 0.4461 (OUTLIER) cc_final: 0.4166 (t60) outliers start: 67 outliers final: 46 residues processed: 171 average time/residue: 0.1623 time to fit residues: 47.2653 Evaluate side-chains 159 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 106 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 275 THR Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 427 MET Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 291 GLU Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 462 MET Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 412 ILE Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 497 ARG Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 282 optimal weight: 6.9990 chunk 197 optimal weight: 40.0000 chunk 305 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 299 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 269 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 163 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS N 411 HIS A 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.114974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.070680 restraints weight = 123281.146| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 6.37 r_work: 0.3007 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 28892 Z= 0.314 Angle : 0.664 9.647 40468 Z= 0.364 Chirality : 0.042 0.179 4708 Planarity : 0.005 0.060 4164 Dihedral : 25.808 176.527 6344 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.60 % Favored : 88.15 % Rotamer: Outliers : 3.55 % Allowed : 30.72 % Favored : 65.73 % 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: -0.80 (0.16), residues: 2845 helix: 1.53 (0.15), residues: 1205 sheet: -1.50 (0.30), residues: 298 loop : -2.36 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.023 0.002 TYR H 80 PHE 0.022 0.001 PHE K 436 TRP 0.007 0.001 TRP N 513 HIS 0.006 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00708 (28892) covalent geometry : angle 0.66440 (40468) hydrogen bonds : bond 0.05369 ( 1274) hydrogen bonds : angle 4.67994 ( 3437) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 105 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 154 PHE cc_start: 0.0644 (OUTLIER) cc_final: -0.0054 (m-80) REVERT: K 250 GLU cc_start: 0.4266 (OUTLIER) cc_final: 0.3838 (tp30) REVERT: K 446 MET cc_start: 0.6286 (mmm) cc_final: 0.6047 (mmt) REVERT: L 477 PHE cc_start: -0.1368 (OUTLIER) cc_final: -0.2863 (t80) REVERT: M 203 MET cc_start: -0.4857 (mtt) cc_final: -0.5146 (mtp) REVERT: N 407 VAL cc_start: -0.1088 (OUTLIER) cc_final: -0.1339 (p) REVERT: N 477 PHE cc_start: -0.1114 (OUTLIER) cc_final: -0.1985 (m-80) REVERT: N 513 TRP cc_start: 0.4257 (OUTLIER) cc_final: 0.3980 (t60) REVERT: A 125 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8586 (mp-120) outliers start: 78 outliers final: 57 residues processed: 178 average time/residue: 0.1552 time to fit residues: 47.6455 Evaluate side-chains 165 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 101 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 286 ILE Chi-restraints excluded: chain K residue 556 LYS Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 275 THR Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 291 GLU Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 455 THR Chi-restraints excluded: chain M residue 462 MET Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 381 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 412 ILE Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 497 ARG Chi-restraints excluded: chain N residue 511 HIS Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 264 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 266 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 208 optimal weight: 20.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN L 103 GLN ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.115904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.071926 restraints weight = 123365.271| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 6.62 r_work: 0.3046 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28892 Z= 0.176 Angle : 0.596 9.619 40468 Z= 0.328 Chirality : 0.039 0.217 4708 Planarity : 0.004 0.060 4164 Dihedral : 25.735 175.165 6344 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.65 % Favored : 89.10 % Rotamer: Outliers : 2.87 % Allowed : 31.41 % Favored : 65.73 % 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: -0.69 (0.16), residues: 2845 helix: 1.61 (0.15), residues: 1211 sheet: -1.40 (0.31), residues: 293 loop : -2.31 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.017 0.001 TYR H 80 PHE 0.020 0.001 PHE K 436 TRP 0.007 0.001 TRP L 513 HIS 0.006 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00392 (28892) covalent geometry : angle 0.59622 (40468) hydrogen bonds : bond 0.04433 ( 1274) hydrogen bonds : angle 4.42353 ( 3437) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 109 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: K 154 PHE cc_start: 0.0814 (OUTLIER) cc_final: 0.0100 (m-80) REVERT: K 250 GLU cc_start: 0.4211 (OUTLIER) cc_final: 0.3792 (tp30) REVERT: K 446 MET cc_start: 0.6277 (mmm) cc_final: 0.6053 (mmt) REVERT: L 477 PHE cc_start: -0.1305 (OUTLIER) cc_final: -0.2714 (t80) REVERT: F 84 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7941 (mmt) REVERT: M 203 MET cc_start: -0.4911 (mtt) cc_final: -0.5189 (mtp) REVERT: N 407 VAL cc_start: -0.0871 (OUTLIER) cc_final: -0.1123 (p) REVERT: N 477 PHE cc_start: -0.1107 (OUTLIER) cc_final: -0.1989 (m-80) REVERT: N 513 TRP cc_start: 0.4299 (OUTLIER) cc_final: 0.4036 (t60) outliers start: 63 outliers final: 49 residues processed: 167 average time/residue: 0.1660 time to fit residues: 47.0377 Evaluate side-chains 165 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 109 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 291 GLU Chi-restraints excluded: chain M residue 455 THR Chi-restraints excluded: chain M residue 462 MET Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 412 ILE Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 497 ARG Chi-restraints excluded: chain N residue 511 HIS Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 263 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 279 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 297 optimal weight: 10.0000 chunk 236 optimal weight: 30.0000 chunk 292 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 GLN ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.116072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.071969 restraints weight = 123186.027| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 6.55 r_work: 0.3055 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28892 Z= 0.177 Angle : 0.592 9.727 40468 Z= 0.325 Chirality : 0.039 0.188 4708 Planarity : 0.004 0.062 4164 Dihedral : 25.645 174.922 6344 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.62 % Favored : 89.14 % Rotamer: Outliers : 2.78 % Allowed : 31.59 % Favored : 65.63 % 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: -0.66 (0.16), residues: 2845 helix: 1.63 (0.15), residues: 1213 sheet: -1.37 (0.31), residues: 293 loop : -2.30 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.016 0.001 TYR G 57 PHE 0.019 0.001 PHE K 436 TRP 0.006 0.001 TRP K 148 HIS 0.006 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00393 (28892) covalent geometry : angle 0.59216 (40468) hydrogen bonds : bond 0.04399 ( 1274) hydrogen bonds : angle 4.38393 ( 3437) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 107 time to evaluate : 0.950 Fit side-chains REVERT: K 154 PHE cc_start: 0.0669 (OUTLIER) cc_final: -0.0048 (m-80) REVERT: K 250 GLU cc_start: 0.4172 (OUTLIER) cc_final: 0.3746 (tp30) REVERT: K 446 MET cc_start: 0.6232 (mmm) cc_final: 0.6006 (mmt) REVERT: L 477 PHE cc_start: -0.1447 (OUTLIER) cc_final: -0.2827 (t80) REVERT: F 84 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7884 (mmt) REVERT: M 203 MET cc_start: -0.4984 (mtt) cc_final: -0.5247 (mtp) REVERT: N 407 VAL cc_start: -0.1061 (OUTLIER) cc_final: -0.1322 (p) REVERT: N 477 PHE cc_start: -0.1149 (OUTLIER) cc_final: -0.2102 (m-80) REVERT: N 513 TRP cc_start: 0.4282 (OUTLIER) cc_final: 0.3987 (t60) outliers start: 61 outliers final: 51 residues processed: 163 average time/residue: 0.1632 time to fit residues: 45.7609 Evaluate side-chains 166 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 108 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 58 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 154 PHE Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 250 GLU Chi-restraints excluded: chain K residue 578 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 103 GLN Chi-restraints excluded: chain L residue 245 ILE Chi-restraints excluded: chain L residue 477 PHE Chi-restraints excluded: chain L residue 499 LEU Chi-restraints excluded: chain L residue 500 HIS Chi-restraints excluded: chain L residue 511 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain M residue 86 VAL Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain M residue 104 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain M residue 267 ILE Chi-restraints excluded: chain M residue 291 GLU Chi-restraints excluded: chain M residue 420 LEU Chi-restraints excluded: chain M residue 455 THR Chi-restraints excluded: chain M residue 462 MET Chi-restraints excluded: chain M residue 506 LEU Chi-restraints excluded: chain M residue 521 LEU Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 80 HIS Chi-restraints excluded: chain N residue 159 ILE Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 GLU Chi-restraints excluded: chain N residue 297 LEU Chi-restraints excluded: chain N residue 311 ILE Chi-restraints excluded: chain N residue 407 VAL Chi-restraints excluded: chain N residue 412 ILE Chi-restraints excluded: chain N residue 473 LEU Chi-restraints excluded: chain N residue 477 PHE Chi-restraints excluded: chain N residue 511 HIS Chi-restraints excluded: chain N residue 513 TRP Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 143 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 293 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 308 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 28 optimal weight: 0.0870 overall best weight: 1.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.116019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.072032 restraints weight = 123017.380| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 6.46 r_work: 0.3059 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28892 Z= 0.179 Angle : 0.594 9.451 40468 Z= 0.325 Chirality : 0.039 0.154 4708 Planarity : 0.004 0.062 4164 Dihedral : 25.598 174.612 6344 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.47 % Favored : 89.28 % Rotamer: Outliers : 2.64 % Allowed : 31.82 % Favored : 65.54 % 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: -0.66 (0.16), residues: 2845 helix: 1.61 (0.15), residues: 1219 sheet: -1.37 (0.31), residues: 293 loop : -2.30 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.016 0.001 TYR H 80 PHE 0.017 0.001 PHE K 436 TRP 0.006 0.001 TRP K 148 HIS 0.006 0.001 HIS M 359 Details of bonding type rmsd covalent geometry : bond 0.00396 (28892) covalent geometry : angle 0.59419 (40468) hydrogen bonds : bond 0.04340 ( 1274) hydrogen bonds : angle 4.36130 ( 3437) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14963.39 seconds wall clock time: 254 minutes 28.26 seconds (15268.26 seconds total)