Starting phenix.real_space_refine on Tue Nov 18 21:15:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c26_7336/11_2025/6c26_7336_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c26_7336/11_2025/6c26_7336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c26_7336/11_2025/6c26_7336_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c26_7336/11_2025/6c26_7336_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c26_7336/11_2025/6c26_7336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c26_7336/11_2025/6c26_7336.map" } resolution = 3.5 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= 0.001 sd= 0.007 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 8 5.49 5 S 55 5.16 5 C 11306 2.51 5 N 2684 2.21 5 O 3135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17188 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5225 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 624} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3496 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 23, 'TRANS': 408} Chain breaks: 2 Chain: "5" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "4" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 259 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "2" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 883 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "3" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1028 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 234} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3218 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 16, 'TRANS': 380} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'EGY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'EGY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'EGY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.93, per 1000 atoms: 0.23 Number of scatterers: 17188 At special positions: 0 Unit cell: (140.352, 130.56, 154.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 8 15.00 O 3135 8.00 N 2684 7.00 C 11306 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 Links applied BETA1-2 " BMA D 3 " - " BMA D 4 " " BMA D 4 " - " BMA D 5 " " BMA D 5 " - " BMA D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " BETA1-6 " BMA D 3 " - " BMA D 7 " NAG-ASN " NAG B 601 " - " ASN B 60 " " NAG D 1 " - " ASN A 539 " " NAG E 1 " - " ASN 1 336 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 815.7 milliseconds 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3946 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 22 sheets defined 41.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 5 through 25 Processing helix chain 'A' and resid 25 through 32 removed outlier: 4.089A pdb=" N ILE A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.727A pdb=" N ILE A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 4.411A pdb=" N ASN A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.519A pdb=" N ASN A 60 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 61 " --> pdb=" O LEU A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 57 through 61' Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.714A pdb=" N LEU A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 68' Processing helix chain 'A' and resid 91 through 104 removed outlier: 3.554A pdb=" N ASN A 103 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 118 through 138 removed outlier: 3.674A pdb=" N PHE A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.500A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 188 removed outlier: 3.514A pdb=" N ALA A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.688A pdb=" N SER A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.671A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.984A pdb=" N THR A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.653A pdb=" N ARG A 262 " --> pdb=" O PHE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.888A pdb=" N PHE A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 356 through 363 removed outlier: 4.250A pdb=" N PHE A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.630A pdb=" N VAL A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 4.335A pdb=" N VAL A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 removed outlier: 4.082A pdb=" N VAL A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 429 removed outlier: 4.320A pdb=" N ILE A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 428 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 473 removed outlier: 3.713A pdb=" N TYR A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 472 " --> pdb=" O TRP A 468 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 removed outlier: 3.565A pdb=" N TYR A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 519 through 527 removed outlier: 3.519A pdb=" N ILE A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 550 Processing helix chain 'A' and resid 553 through 563 removed outlier: 4.558A pdb=" N GLU A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 594 removed outlier: 3.871A pdb=" N MET A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 591 " --> pdb=" O PHE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.785A pdb=" N LYS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 627 through 632' Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.774A pdb=" N GLY A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN A 645 " --> pdb=" O ASN A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 641 through 645' Processing helix chain 'A' and resid 691 through 701 removed outlier: 3.744A pdb=" N GLY A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain '1' and resid 191 through 195 removed outlier: 3.711A pdb=" N LEU 1 194 " --> pdb=" O ASP 1 191 " (cutoff:3.500A) Processing helix chain '1' and resid 269 through 279 removed outlier: 3.912A pdb=" N LEU 1 273 " --> pdb=" O SER 1 269 " (cutoff:3.500A) Processing helix chain '1' and resid 344 through 347 removed outlier: 3.981A pdb=" N ASP 1 347 " --> pdb=" O LYS 1 344 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 344 through 347' Processing helix chain '1' and resid 442 through 447 removed outlier: 4.012A pdb=" N PHE 1 447 " --> pdb=" O LYS 1 443 " (cutoff:3.500A) Processing helix chain '1' and resid 448 through 469 removed outlier: 3.746A pdb=" N MET 1 462 " --> pdb=" O PHE 1 458 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY 1 463 " --> pdb=" O THR 1 459 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL 1 464 " --> pdb=" O ALA 1 460 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 12 removed outlier: 3.696A pdb=" N HIS 5 11 " --> pdb=" O TYR 5 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER 5 12 " --> pdb=" O LYS 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 24 through 46 removed outlier: 3.868A pdb=" N PHE 5 28 " --> pdb=" O THR 5 24 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE 5 30 " --> pdb=" O PRO 5 26 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE 5 34 " --> pdb=" O ILE 5 30 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL 5 35 " --> pdb=" O CYS 5 31 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU 5 37 " --> pdb=" O LEU 5 33 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA 5 46 " --> pdb=" O SER 5 42 " (cutoff:3.500A) Processing helix chain '5' and resid 52 through 80 removed outlier: 4.256A pdb=" N LEU 5 73 " --> pdb=" O LEU 5 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN 5 80 " --> pdb=" O VAL 5 76 " (cutoff:3.500A) Processing helix chain '4' and resid 3 through 32 removed outlier: 3.517A pdb=" N LEU 4 7 " --> pdb=" O SER 4 3 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU 4 21 " --> pdb=" O VAL 4 17 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE 4 22 " --> pdb=" O MET 4 18 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL 4 23 " --> pdb=" O MET 4 19 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE 4 24 " --> pdb=" O THR 4 20 " (cutoff:3.500A) Processing helix chain '2' and resid 23 through 41 removed outlier: 3.848A pdb=" N GLN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR 2 41 " --> pdb=" O GLN 2 37 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 68 removed outlier: 3.909A pdb=" N PHE 2 53 " --> pdb=" O THR 2 49 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY 2 58 " --> pdb=" O LEU 2 54 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE 2 65 " --> pdb=" O GLN 2 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE 2 68 " --> pdb=" O PHE 2 64 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 100 removed outlier: 4.177A pdb=" N GLY 2 80 " --> pdb=" O ALA 2 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE 2 81 " --> pdb=" O PHE 2 77 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 2 91 " --> pdb=" O GLN 2 87 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN 2 100 " --> pdb=" O LEU 2 96 " (cutoff:3.500A) Processing helix chain '2' and resid 108 through 125 removed outlier: 3.929A pdb=" N ALA 2 112 " --> pdb=" O ASN 2 108 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU 2 121 " --> pdb=" O ALA 2 117 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS 2 122 " --> pdb=" O SER 2 118 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE 2 123 " --> pdb=" O LEU 2 119 " (cutoff:3.500A) Processing helix chain '3' and resid 209 through 216 Processing helix chain '3' and resid 217 through 233 removed outlier: 3.695A pdb=" N SER 3 233 " --> pdb=" O ILE 3 229 " (cutoff:3.500A) Processing helix chain '3' and resid 234 through 241 removed outlier: 3.897A pdb=" N ASN 3 238 " --> pdb=" O ALA 3 234 " (cutoff:3.500A) Processing helix chain '3' and resid 268 through 289 removed outlier: 3.654A pdb=" N VAL 3 272 " --> pdb=" O ILE 3 268 " (cutoff:3.500A) Processing helix chain '3' and resid 291 through 297 removed outlier: 3.584A pdb=" N ARG 3 295 " --> pdb=" O ILE 3 291 " (cutoff:3.500A) Processing helix chain '3' and resid 305 through 335 removed outlier: 3.773A pdb=" N ASP 3 309 " --> pdb=" O ALA 3 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.533A pdb=" N GLU C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 217 removed outlier: 3.936A pdb=" N LEU C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 217 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 254 removed outlier: 3.806A pdb=" N PHE C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 254 " --> pdb=" O ARG C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 283 removed outlier: 3.984A pdb=" N THR C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) Proline residue: C 270 - end of helix removed outlier: 3.581A pdb=" N GLY C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 50 removed outlier: 3.841A pdb=" N LEU B 44 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.846A pdb=" N ALA B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 104 removed outlier: 3.561A pdb=" N LEU B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.648A pdb=" N ALA B 250 " --> pdb=" O ASN B 246 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 412 removed outlier: 3.862A pdb=" N ILE B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 71 removed outlier: 3.582A pdb=" N ASP A 71 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 80 " --> pdb=" O ASP A 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 531 removed outlier: 3.633A pdb=" N VAL A 513 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS A 512 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 570 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA A 514 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ILE A 572 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 670 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN A 681 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU A 668 " --> pdb=" O GLN A 681 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AA4, first strand: chain '1' and resid 129 through 136 removed outlier: 6.777A pdb=" N SER 1 48 " --> pdb=" O ILE 1 40 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE 1 40 " --> pdb=" O SER 1 48 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR 1 50 " --> pdb=" O ARG 1 38 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG 1 38 " --> pdb=" O THR 1 50 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU 1 52 " --> pdb=" O TYR 1 36 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR 1 36 " --> pdb=" O GLU 1 52 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR 1 54 " --> pdb=" O VAL 1 34 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU 1 32 " --> pdb=" O LYS 1 56 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N SER 1 174 " --> pdb=" O VAL 1 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR 1 36 " --> pdb=" O SER 1 174 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR 1 176 " --> pdb=" O TYR 1 36 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG 1 38 " --> pdb=" O THR 1 176 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE 1 178 " --> pdb=" O ARG 1 38 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE 1 40 " --> pdb=" O ILE 1 178 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU 1 177 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 66 through 70 removed outlier: 3.556A pdb=" N GLN 1 95 " --> pdb=" O ILE 1 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 142 through 143 removed outlier: 3.721A pdb=" N GLN 1 154 " --> pdb=" O HIS 1 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 426 through 427 removed outlier: 9.159A pdb=" N GLN 1 232 " --> pdb=" O TYR 1 374 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN 1 376 " --> pdb=" O GLN 1 232 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 1 234 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU 1 378 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 1 236 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER 1 380 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG 1 238 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE 1 382 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 1 240 " --> pdb=" O PHE 1 382 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 231 through 242 current: chain '1' and resid 303 through 305 Processing sheet with id=AA8, first strand: chain '1' and resid 401 through 406 removed outlier: 3.522A pdb=" N VAL 1 417 " --> pdb=" O LEU 1 383 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N GLN 1 232 " --> pdb=" O TYR 1 374 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN 1 376 " --> pdb=" O GLN 1 232 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 1 234 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU 1 378 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 1 236 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER 1 380 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG 1 238 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE 1 382 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 1 240 " --> pdb=" O PHE 1 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '1' and resid 303 through 305 removed outlier: 3.541A pdb=" N GLY 1 340 " --> pdb=" O TYR 1 303 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR 1 338 " --> pdb=" O THR 1 305 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N GLN 1 232 " --> pdb=" O TYR 1 374 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN 1 376 " --> pdb=" O GLN 1 232 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 1 234 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU 1 378 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 1 236 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER 1 380 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG 1 238 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE 1 382 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 1 240 " --> pdb=" O PHE 1 382 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1' and resid 255 through 259 removed outlier: 9.159A pdb=" N GLN 1 232 " --> pdb=" O TYR 1 374 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN 1 376 " --> pdb=" O GLN 1 232 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL 1 234 " --> pdb=" O ASN 1 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU 1 378 " --> pdb=" O VAL 1 234 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 1 236 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N SER 1 380 " --> pdb=" O LEU 1 236 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ARG 1 238 " --> pdb=" O SER 1 380 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N PHE 1 382 " --> pdb=" O ARG 1 238 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE 1 240 " --> pdb=" O PHE 1 382 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL 1 417 " --> pdb=" O LEU 1 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 291 through 294 removed outlier: 3.785A pdb=" N MET 1 293 " --> pdb=" O PHE 1 321 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE 1 321 " --> pdb=" O MET 1 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE 1 322 " --> pdb=" O HIS 1 315 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS 1 315 " --> pdb=" O PHE 1 322 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 349 through 351 removed outlier: 3.860A pdb=" N ASP 1 391 " --> pdb=" O LYS 1 438 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP 1 440 " --> pdb=" O ILE 1 389 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE 1 389 " --> pdb=" O ASP 1 440 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB5, first strand: chain 'C' and resid 92 through 96 removed outlier: 6.976A pdb=" N ALA C 135 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 137 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 152 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 29 removed outlier: 5.185A pdb=" N MET B 112 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE B 216 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN B 193 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 218 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AB8, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AB9, first strand: chain 'B' and resid 139 through 142 removed outlier: 3.531A pdb=" N ARG B 141 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 199 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 151 through 154 removed outlier: 3.580A pdb=" N LEU B 151 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 263 through 273 removed outlier: 4.329A pdb=" N VAL B 263 " --> pdb=" O TRP B 299 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 299 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 295 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA B 269 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 293 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N HIS B 271 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE B 291 " --> pdb=" O HIS B 271 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N HIS B 273 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LYS B 289 " --> pdb=" O HIS B 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AC4, first strand: chain 'B' and resid 321 through 326 removed outlier: 3.706A pdb=" N TYR B 323 " --> pdb=" O LEU B 316 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2642 1.30 - 1.43: 5072 1.43 - 1.56: 9788 1.56 - 1.69: 33 1.69 - 1.82: 92 Bond restraints: 17627 Sorted by residual: bond pdb=" C2 BMA D 4 " pdb=" O2 BMA D 4 " ideal model delta sigma weight residual 1.402 1.566 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" C1 BMA D 4 " pdb=" C2 BMA D 4 " ideal model delta sigma weight residual 1.519 1.634 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.632 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C2 BMA D 5 " pdb=" O2 BMA D 5 " ideal model delta sigma weight residual 1.402 1.509 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C21 EGY C 301 " pdb=" O21 EGY C 301 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 17622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 23472 4.58 - 9.16: 357 9.16 - 13.74: 43 13.74 - 18.32: 10 18.32 - 22.90: 3 Bond angle restraints: 23885 Sorted by residual: angle pdb=" C TYR A 76 " pdb=" N PRO A 77 " pdb=" CA PRO A 77 " ideal model delta sigma weight residual 119.56 103.90 15.66 1.01e+00 9.80e-01 2.41e+02 angle pdb=" N GLU 1 209 " pdb=" CA GLU 1 209 " pdb=" C GLU 1 209 " ideal model delta sigma weight residual 111.28 120.85 -9.57 1.09e+00 8.42e-01 7.71e+01 angle pdb=" C LEU B 346 " pdb=" N PRO B 347 " pdb=" CA PRO B 347 " ideal model delta sigma weight residual 119.92 129.02 -9.10 1.07e+00 8.73e-01 7.24e+01 angle pdb=" N ILE A 278 " pdb=" CA ILE A 278 " pdb=" C ILE A 278 " ideal model delta sigma weight residual 110.62 118.99 -8.37 1.02e+00 9.61e-01 6.74e+01 angle pdb=" N TYR A 76 " pdb=" CA TYR A 76 " pdb=" C TYR A 76 " ideal model delta sigma weight residual 113.45 123.89 -10.44 1.39e+00 5.18e-01 5.64e+01 ... (remaining 23880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.72: 10097 31.72 - 63.45: 296 63.45 - 95.17: 97 95.17 - 126.90: 34 126.90 - 158.62: 5 Dihedral angle restraints: 10529 sinusoidal: 4429 harmonic: 6100 Sorted by residual: dihedral pdb=" CA TYR 1 84 " pdb=" C TYR 1 84 " pdb=" N PHE 1 85 " pdb=" CA PHE 1 85 " ideal model delta harmonic sigma weight residual 180.00 151.64 28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ASN A 60 " pdb=" C ASN A 60 " pdb=" N ASN A 61 " pdb=" CA ASN A 61 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASN B 225 " pdb=" C ASN B 225 " pdb=" N ASN B 226 " pdb=" CA ASN B 226 " ideal model delta harmonic sigma weight residual -180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 10526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2214 0.086 - 0.173: 389 0.173 - 0.259: 63 0.259 - 0.345: 17 0.345 - 0.431: 5 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA TYR A 76 " pdb=" N TYR A 76 " pdb=" C TYR A 76 " pdb=" CB TYR A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" C2 BMA D 3 " pdb=" C1 BMA D 3 " pdb=" C3 BMA D 3 " pdb=" O2 BMA D 3 " both_signs ideal model delta sigma weight residual False 2.47 2.90 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" N2 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 2685 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA 3 234 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C ALA 3 234 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA 3 234 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR 3 235 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 597 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ILE A 597 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 597 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP A 598 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 398 " 0.016 2.00e-02 2.50e+03 2.14e-02 8.01e+00 pdb=" CG PHE 1 398 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 398 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 398 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 398 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 398 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 1 398 " 0.001 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 49 2.45 - 3.06: 10216 3.06 - 3.67: 23568 3.67 - 4.29: 32830 4.29 - 4.90: 56324 Nonbonded interactions: 122987 Sorted by model distance: nonbonded pdb=" NZ LYS C 77 " pdb=" OG1 THR C 143 " model vdw 1.833 3.120 nonbonded pdb=" OH TYR B 69 " pdb=" ND2 ASN B 105 " model vdw 1.955 3.120 nonbonded pdb=" O LYS 1 171 " pdb=" O GLU 1 209 " model vdw 2.001 3.040 nonbonded pdb=" O PRO B 321 " pdb=" O4 BMA D 4 " model vdw 2.131 3.040 nonbonded pdb=" CG2 ILE B 291 " pdb=" O GLY B 342 " model vdw 2.139 3.460 ... (remaining 122982 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.011 0.164 17638 Z= 0.503 Angle : 1.422 22.899 23918 Z= 0.707 Chirality : 0.073 0.431 2688 Planarity : 0.008 0.067 2928 Dihedral : 18.345 158.619 6583 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.79 % Favored : 90.16 % Rotamer: Outliers : 2.07 % Allowed : 7.15 % Favored : 90.78 % 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: -4.59 (0.14), residues: 2043 helix: -2.90 (0.13), residues: 779 sheet: -2.07 (0.27), residues: 353 loop : -3.55 (0.15), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 690 TYR 0.034 0.003 TYR 3 277 PHE 0.049 0.004 PHE 1 398 TRP 0.040 0.004 TRP A 675 HIS 0.011 0.002 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.01140 (17627) covalent geometry : angle 1.40738 (23885) hydrogen bonds : bond 0.18032 ( 627) hydrogen bonds : angle 8.51597 ( 1866) link_BETA1-2 : bond 0.03369 ( 3) link_BETA1-2 : angle 7.72061 ( 9) link_BETA1-4 : bond 0.02083 ( 4) link_BETA1-4 : angle 5.15989 ( 12) link_BETA1-6 : bond 0.04217 ( 1) link_BETA1-6 : angle 4.18393 ( 3) link_NAG-ASN : bond 0.01720 ( 3) link_NAG-ASN : angle 4.16082 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 378 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 135 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7838 (ttmt) REVERT: A 286 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7537 (ttpt) REVERT: A 383 ASP cc_start: 0.7551 (t0) cc_final: 0.7326 (t0) REVERT: A 402 MET cc_start: 0.7752 (mpt) cc_final: 0.7371 (mpt) REVERT: A 481 LEU cc_start: 0.8375 (mm) cc_final: 0.7697 (tt) REVERT: A 565 ASP cc_start: 0.8409 (t0) cc_final: 0.8025 (t70) REVERT: A 583 ASP cc_start: 0.8796 (t70) cc_final: 0.8527 (m-30) REVERT: 1 84 TYR cc_start: 0.7664 (m-80) cc_final: 0.7427 (m-10) REVERT: 1 95 GLN cc_start: 0.7840 (pm20) cc_final: 0.7554 (pt0) REVERT: 1 203 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7513 (m-10) REVERT: 1 424 ARG cc_start: 0.7704 (ttm-80) cc_final: 0.7493 (mtp85) REVERT: 5 7 TYR cc_start: 0.8736 (t80) cc_final: 0.8449 (t80) REVERT: 2 67 LEU cc_start: 0.8501 (tp) cc_final: 0.8273 (tt) REVERT: 3 255 MET cc_start: 0.5789 (tpp) cc_final: 0.5468 (tpt) REVERT: C 275 SER cc_start: 0.8715 (m) cc_final: 0.8409 (p) REVERT: B 106 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7882 (mp0) REVERT: B 159 LEU cc_start: 0.8906 (mm) cc_final: 0.8659 (mp) REVERT: B 325 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8674 (pp) REVERT: B 348 ASP cc_start: 0.7990 (t0) cc_final: 0.7677 (t0) REVERT: B 415 THR cc_start: 0.9553 (m) cc_final: 0.9059 (p) outliers start: 38 outliers final: 18 residues processed: 408 average time/residue: 0.1420 time to fit residues: 84.8885 Evaluate side-chains 228 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 2 residue 95 ARG Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 193 HIS A 266 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 540 ASN A 674 ASN 1 284 GLN 1 343 ASN ** 1 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 222 GLN B 259 ASN B 307 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109283 restraints weight = 23877.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107770 restraints weight = 35673.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108673 restraints weight = 36560.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110655 restraints weight = 24261.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110846 restraints weight = 17766.646| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17638 Z= 0.181 Angle : 0.788 14.240 23918 Z= 0.386 Chirality : 0.049 0.411 2688 Planarity : 0.006 0.057 2928 Dihedral : 18.696 156.451 2781 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.75 % Allowed : 11.18 % Favored : 84.07 % 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: -3.30 (0.16), residues: 2043 helix: -1.10 (0.17), residues: 801 sheet: -1.96 (0.27), residues: 361 loop : -3.33 (0.16), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 262 TYR 0.022 0.002 TYR 3 235 PHE 0.042 0.002 PHE 1 398 TRP 0.021 0.002 TRP A 208 HIS 0.005 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00403 (17627) covalent geometry : angle 0.76882 (23885) hydrogen bonds : bond 0.06835 ( 627) hydrogen bonds : angle 5.20132 ( 1866) link_BETA1-2 : bond 0.03168 ( 3) link_BETA1-2 : angle 6.99970 ( 9) link_BETA1-4 : bond 0.02271 ( 4) link_BETA1-4 : angle 3.97558 ( 12) link_BETA1-6 : bond 0.01071 ( 1) link_BETA1-6 : angle 3.19201 ( 3) link_NAG-ASN : bond 0.01307 ( 3) link_NAG-ASN : angle 2.50061 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 232 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.8071 (t80) cc_final: 0.7130 (m-10) REVERT: A 122 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8060 (m-80) REVERT: A 217 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8291 (tt) REVERT: A 383 ASP cc_start: 0.7431 (t0) cc_final: 0.7218 (t0) REVERT: A 412 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 481 LEU cc_start: 0.8493 (mm) cc_final: 0.7911 (tt) REVERT: A 495 ASP cc_start: 0.8465 (p0) cc_final: 0.8215 (p0) REVERT: A 565 ASP cc_start: 0.8112 (t0) cc_final: 0.7741 (t70) REVERT: A 663 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7608 (pp) REVERT: A 676 MET cc_start: 0.7762 (ttm) cc_final: 0.7331 (ttm) REVERT: 1 197 LYS cc_start: 0.7722 (mttt) cc_final: 0.7460 (ptmt) REVERT: 1 203 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7865 (m-10) REVERT: 1 209 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: 1 242 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8552 (tt) REVERT: 1 371 ASP cc_start: 0.7444 (t0) cc_final: 0.7210 (t0) REVERT: 5 7 TYR cc_start: 0.8724 (t80) cc_final: 0.8453 (t80) REVERT: 4 14 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: 2 98 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8305 (tp) REVERT: 3 255 MET cc_start: 0.5836 (tpp) cc_final: 0.5568 (tpt) REVERT: C 275 SER cc_start: 0.8985 (m) cc_final: 0.8396 (p) REVERT: B 112 MET cc_start: 0.8213 (ptp) cc_final: 0.7916 (ptm) REVERT: B 325 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8631 (pp) REVERT: B 348 ASP cc_start: 0.8135 (t0) cc_final: 0.7818 (t0) outliers start: 87 outliers final: 40 residues processed: 306 average time/residue: 0.1271 time to fit residues: 60.3396 Evaluate side-chains 238 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 177 LEU Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 1 residue 430 VAL Chi-restraints excluded: chain 1 residue 466 VAL Chi-restraints excluded: chain 5 residue 69 LEU Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 66 ILE Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 216 ASN ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 425 ASN 5 17 GLN 2 61 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.135509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106501 restraints weight = 24367.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106220 restraints weight = 38267.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106984 restraints weight = 38864.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.108720 restraints weight = 25589.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108812 restraints weight = 20478.791| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17638 Z= 0.185 Angle : 0.747 13.820 23918 Z= 0.362 Chirality : 0.048 0.383 2688 Planarity : 0.005 0.068 2928 Dihedral : 16.302 159.683 2762 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.75 % Allowed : 13.69 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.17), residues: 2043 helix: -0.15 (0.18), residues: 808 sheet: -1.79 (0.27), residues: 349 loop : -3.10 (0.17), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 37 TYR 0.016 0.001 TYR 2 41 PHE 0.050 0.002 PHE 1 398 TRP 0.012 0.001 TRP A 49 HIS 0.006 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00435 (17627) covalent geometry : angle 0.72810 (23885) hydrogen bonds : bond 0.06326 ( 627) hydrogen bonds : angle 4.62891 ( 1866) link_BETA1-2 : bond 0.02869 ( 3) link_BETA1-2 : angle 6.60222 ( 9) link_BETA1-4 : bond 0.01820 ( 4) link_BETA1-4 : angle 4.20259 ( 12) link_BETA1-6 : bond 0.00622 ( 1) link_BETA1-6 : angle 3.03430 ( 3) link_NAG-ASN : bond 0.01202 ( 3) link_NAG-ASN : angle 2.40167 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 207 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 25 PHE cc_start: 0.8075 (t80) cc_final: 0.7061 (m-10) REVERT: A 122 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: A 217 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8178 (tt) REVERT: A 383 ASP cc_start: 0.7570 (t0) cc_final: 0.7339 (t0) REVERT: A 402 MET cc_start: 0.8111 (mpt) cc_final: 0.7760 (mpt) REVERT: A 412 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8813 (p) REVERT: A 481 LEU cc_start: 0.8541 (mm) cc_final: 0.8071 (tp) REVERT: A 565 ASP cc_start: 0.8089 (t0) cc_final: 0.7685 (t70) REVERT: A 663 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7557 (pp) REVERT: A 676 MET cc_start: 0.7982 (ttm) cc_final: 0.7658 (ttm) REVERT: 1 55 ILE cc_start: 0.8441 (pt) cc_final: 0.8081 (mt) REVERT: 1 165 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8496 (tt) REVERT: 1 197 LYS cc_start: 0.7753 (mttt) cc_final: 0.7449 (ptmt) REVERT: 1 209 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: 1 242 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8555 (tt) REVERT: 5 7 TYR cc_start: 0.8692 (t80) cc_final: 0.8425 (t80) REVERT: 4 14 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: 2 28 LYS cc_start: 0.7539 (ptpp) cc_final: 0.7268 (ptpp) REVERT: 2 98 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8344 (tp) REVERT: 3 255 MET cc_start: 0.5919 (tpp) cc_final: 0.5607 (tpt) REVERT: C 69 ASN cc_start: 0.8068 (t0) cc_final: 0.7730 (t0) REVERT: C 275 SER cc_start: 0.8980 (m) cc_final: 0.8454 (p) REVERT: B 325 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8572 (pp) REVERT: B 348 ASP cc_start: 0.8168 (t0) cc_final: 0.7859 (t0) outliers start: 87 outliers final: 49 residues processed: 279 average time/residue: 0.1329 time to fit residues: 56.6237 Evaluate side-chains 253 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 79 SER Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 466 VAL Chi-restraints excluded: chain 5 residue 69 LEU Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 63 THR Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 332 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 5 optimal weight: 0.4980 chunk 185 optimal weight: 4.9990 chunk 201 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 HIS 1 280 GLN 2 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110071 restraints weight = 24144.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109465 restraints weight = 37730.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110881 restraints weight = 32423.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111470 restraints weight = 22441.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111976 restraints weight = 22371.660| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17638 Z= 0.129 Angle : 0.676 11.802 23918 Z= 0.324 Chirality : 0.046 0.397 2688 Planarity : 0.004 0.056 2928 Dihedral : 14.815 160.999 2759 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.09 % Allowed : 15.11 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.18), residues: 2043 helix: 0.51 (0.19), residues: 811 sheet: -1.61 (0.28), residues: 341 loop : -2.98 (0.17), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 649 TYR 0.013 0.001 TYR 2 41 PHE 0.023 0.001 PHE 1 398 TRP 0.013 0.001 TRP B 299 HIS 0.003 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00279 (17627) covalent geometry : angle 0.65742 (23885) hydrogen bonds : bond 0.04969 ( 627) hydrogen bonds : angle 4.24003 ( 1866) link_BETA1-2 : bond 0.02676 ( 3) link_BETA1-2 : angle 6.25585 ( 9) link_BETA1-4 : bond 0.01513 ( 4) link_BETA1-4 : angle 3.96405 ( 12) link_BETA1-6 : bond 0.00811 ( 1) link_BETA1-6 : angle 2.54841 ( 3) link_NAG-ASN : bond 0.01119 ( 3) link_NAG-ASN : angle 2.06975 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 214 time to evaluate : 0.697 Fit side-chains REVERT: A 122 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: A 217 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8130 (tt) REVERT: A 383 ASP cc_start: 0.7541 (t0) cc_final: 0.7329 (t0) REVERT: A 397 TYR cc_start: 0.8322 (t80) cc_final: 0.8110 (t80) REVERT: A 402 MET cc_start: 0.8104 (mpt) cc_final: 0.7691 (mpt) REVERT: A 412 VAL cc_start: 0.9116 (OUTLIER) cc_final: 0.8723 (p) REVERT: A 481 LEU cc_start: 0.8519 (mm) cc_final: 0.8036 (tp) REVERT: A 495 ASP cc_start: 0.8343 (p0) cc_final: 0.8071 (m-30) REVERT: A 565 ASP cc_start: 0.8106 (t0) cc_final: 0.7739 (t70) REVERT: A 663 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7459 (pp) REVERT: A 676 MET cc_start: 0.8007 (ttm) cc_final: 0.7805 (ttm) REVERT: 1 165 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8483 (tt) REVERT: 1 197 LYS cc_start: 0.7740 (mttt) cc_final: 0.7454 (ptmt) REVERT: 1 209 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: 1 242 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8487 (tt) REVERT: 5 7 TYR cc_start: 0.8673 (t80) cc_final: 0.8460 (t80) REVERT: 4 14 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: 2 28 LYS cc_start: 0.7549 (ptpp) cc_final: 0.7280 (ptpp) REVERT: 2 98 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8281 (tp) REVERT: 3 255 MET cc_start: 0.5655 (tpp) cc_final: 0.5330 (tpt) REVERT: C 69 ASN cc_start: 0.8234 (t0) cc_final: 0.7910 (t0) REVERT: C 216 ASN cc_start: 0.8394 (t0) cc_final: 0.8171 (t0) REVERT: C 275 SER cc_start: 0.9013 (m) cc_final: 0.8531 (p) REVERT: B 325 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8506 (pp) REVERT: B 348 ASP cc_start: 0.8111 (t0) cc_final: 0.7877 (t0) outliers start: 75 outliers final: 48 residues processed: 272 average time/residue: 0.1268 time to fit residues: 53.5512 Evaluate side-chains 253 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 177 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 195 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 242 LEU Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 55 VAL Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 124 VAL Chi-restraints excluded: chain 3 residue 293 PHE Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 158 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 99 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110421 restraints weight = 23953.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110314 restraints weight = 38184.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111517 restraints weight = 33424.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111802 restraints weight = 22919.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112284 restraints weight = 23651.506| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17638 Z= 0.124 Angle : 0.651 11.383 23918 Z= 0.312 Chirality : 0.046 0.386 2688 Planarity : 0.004 0.061 2928 Dihedral : 14.070 162.100 2759 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.64 % Allowed : 15.77 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.18), residues: 2043 helix: 0.90 (0.19), residues: 809 sheet: -1.44 (0.29), residues: 338 loop : -2.84 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 649 TYR 0.023 0.001 TYR 2 41 PHE 0.012 0.001 PHE B 409 TRP 0.012 0.001 TRP B 299 HIS 0.003 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00272 (17627) covalent geometry : angle 0.63359 (23885) hydrogen bonds : bond 0.04660 ( 627) hydrogen bonds : angle 4.06802 ( 1866) link_BETA1-2 : bond 0.02427 ( 3) link_BETA1-2 : angle 5.89974 ( 9) link_BETA1-4 : bond 0.01413 ( 4) link_BETA1-4 : angle 3.91467 ( 12) link_BETA1-6 : bond 0.00795 ( 1) link_BETA1-6 : angle 2.44692 ( 3) link_NAG-ASN : bond 0.00972 ( 3) link_NAG-ASN : angle 1.97208 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 212 time to evaluate : 0.694 Fit side-chains REVERT: A 122 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: A 217 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8097 (tt) REVERT: A 368 TRP cc_start: 0.8177 (OUTLIER) cc_final: 0.7819 (t60) REVERT: A 383 ASP cc_start: 0.7529 (t0) cc_final: 0.7325 (t0) REVERT: A 397 TYR cc_start: 0.8343 (t80) cc_final: 0.8140 (t80) REVERT: A 412 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 481 LEU cc_start: 0.8527 (mm) cc_final: 0.8039 (tp) REVERT: A 510 ASP cc_start: 0.7268 (p0) cc_final: 0.7031 (p0) REVERT: A 528 ASP cc_start: 0.8244 (t0) cc_final: 0.7967 (t0) REVERT: A 565 ASP cc_start: 0.8117 (t0) cc_final: 0.7733 (t0) REVERT: A 663 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7376 (pp) REVERT: A 676 MET cc_start: 0.8016 (ttm) cc_final: 0.7800 (ttm) REVERT: 1 55 ILE cc_start: 0.8412 (pt) cc_final: 0.8052 (mt) REVERT: 1 165 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8477 (tt) REVERT: 1 197 LYS cc_start: 0.7696 (mttt) cc_final: 0.7392 (ptmt) REVERT: 1 209 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: 1 253 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8256 (mm-30) REVERT: 1 418 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8572 (ttpt) REVERT: 4 14 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: 2 28 LYS cc_start: 0.7560 (ptpp) cc_final: 0.7353 (ptpp) REVERT: 2 98 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8189 (tp) REVERT: 3 210 MET cc_start: 0.6989 (mmm) cc_final: 0.6601 (mmt) REVERT: 3 255 MET cc_start: 0.5667 (tpp) cc_final: 0.5379 (tpt) REVERT: C 216 ASN cc_start: 0.8407 (t0) cc_final: 0.8168 (t0) REVERT: C 275 SER cc_start: 0.9072 (m) cc_final: 0.8544 (p) REVERT: B 325 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8479 (pp) REVERT: B 348 ASP cc_start: 0.8134 (t0) cc_final: 0.7928 (t0) outliers start: 85 outliers final: 53 residues processed: 280 average time/residue: 0.1252 time to fit residues: 55.0023 Evaluate side-chains 259 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 177 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 195 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 66 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 140 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 99 optimal weight: 0.0050 chunk 62 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109929 restraints weight = 24027.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109166 restraints weight = 37102.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110524 restraints weight = 33151.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110776 restraints weight = 23533.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111316 restraints weight = 23784.356| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17638 Z= 0.136 Angle : 0.653 11.094 23918 Z= 0.313 Chirality : 0.046 0.379 2688 Planarity : 0.004 0.061 2928 Dihedral : 13.552 161.917 2758 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.07 % Allowed : 15.98 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.18), residues: 2043 helix: 1.12 (0.19), residues: 808 sheet: -1.30 (0.29), residues: 338 loop : -2.77 (0.18), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 649 TYR 0.017 0.001 TYR 2 41 PHE 0.019 0.001 PHE 1 398 TRP 0.013 0.001 TRP B 299 HIS 0.004 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00310 (17627) covalent geometry : angle 0.63610 (23885) hydrogen bonds : bond 0.04792 ( 627) hydrogen bonds : angle 3.96996 ( 1866) link_BETA1-2 : bond 0.02413 ( 3) link_BETA1-2 : angle 5.56374 ( 9) link_BETA1-4 : bond 0.01380 ( 4) link_BETA1-4 : angle 4.03581 ( 12) link_BETA1-6 : bond 0.00710 ( 1) link_BETA1-6 : angle 2.42110 ( 3) link_NAG-ASN : bond 0.00960 ( 3) link_NAG-ASN : angle 1.93313 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 196 time to evaluate : 0.731 Fit side-chains REVERT: A 122 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: A 217 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8165 (tt) REVERT: A 368 TRP cc_start: 0.8085 (OUTLIER) cc_final: 0.7622 (t60) REVERT: A 383 ASP cc_start: 0.7545 (t0) cc_final: 0.7327 (t0) REVERT: A 397 TYR cc_start: 0.8313 (t80) cc_final: 0.8081 (t80) REVERT: A 412 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8663 (p) REVERT: A 481 LEU cc_start: 0.8537 (mm) cc_final: 0.8064 (tp) REVERT: A 510 ASP cc_start: 0.7274 (p0) cc_final: 0.7020 (p0) REVERT: A 528 ASP cc_start: 0.8252 (t0) cc_final: 0.7990 (t0) REVERT: A 565 ASP cc_start: 0.8066 (t0) cc_final: 0.7710 (t0) REVERT: A 663 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7542 (pp) REVERT: 1 165 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8492 (tt) REVERT: 1 197 LYS cc_start: 0.7704 (mttt) cc_final: 0.7480 (ptmt) REVERT: 1 209 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: 1 244 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8369 (t-90) REVERT: 1 253 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8241 (mm-30) REVERT: 1 418 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8624 (ttpt) REVERT: 4 14 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: 2 28 LYS cc_start: 0.7562 (ptpp) cc_final: 0.7352 (ptpp) REVERT: 2 98 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8267 (tp) REVERT: 3 210 MET cc_start: 0.6941 (mmm) cc_final: 0.6430 (mmt) REVERT: 3 214 ILE cc_start: 0.8220 (tt) cc_final: 0.7990 (tt) REVERT: 3 255 MET cc_start: 0.5667 (tpp) cc_final: 0.5383 (tpt) REVERT: C 69 ASN cc_start: 0.7712 (t0) cc_final: 0.7507 (t0) REVERT: C 109 TYR cc_start: 0.8331 (m-10) cc_final: 0.8113 (m-10) REVERT: C 275 SER cc_start: 0.9174 (m) cc_final: 0.8680 (p) REVERT: B 325 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8608 (pp) outliers start: 93 outliers final: 63 residues processed: 272 average time/residue: 0.1238 time to fit residues: 53.2833 Evaluate side-chains 263 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 188 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 177 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 244 HIS Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 1 residue 455 CYS Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 124 VAL Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 51 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.110293 restraints weight = 24011.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110131 restraints weight = 39317.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111152 restraints weight = 34001.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112475 restraints weight = 23562.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112749 restraints weight = 21541.159| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17638 Z= 0.123 Angle : 0.639 10.901 23918 Z= 0.305 Chirality : 0.045 0.372 2688 Planarity : 0.004 0.075 2928 Dihedral : 13.081 162.340 2758 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.42 % Allowed : 16.53 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 2043 helix: 1.36 (0.19), residues: 804 sheet: -1.18 (0.29), residues: 339 loop : -2.68 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 349 TYR 0.014 0.001 TYR 2 41 PHE 0.015 0.001 PHE 1 398 TRP 0.012 0.001 TRP B 299 HIS 0.003 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00272 (17627) covalent geometry : angle 0.62346 (23885) hydrogen bonds : bond 0.04424 ( 627) hydrogen bonds : angle 3.87527 ( 1866) link_BETA1-2 : bond 0.02305 ( 3) link_BETA1-2 : angle 5.35531 ( 9) link_BETA1-4 : bond 0.01272 ( 4) link_BETA1-4 : angle 3.91465 ( 12) link_BETA1-6 : bond 0.00762 ( 1) link_BETA1-6 : angle 2.25600 ( 3) link_NAG-ASN : bond 0.00916 ( 3) link_NAG-ASN : angle 1.84380 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 210 time to evaluate : 0.687 Fit side-chains REVERT: A 122 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: A 217 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8177 (tt) REVERT: A 368 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.7517 (t60) REVERT: A 383 ASP cc_start: 0.7531 (t0) cc_final: 0.7327 (t0) REVERT: A 397 TYR cc_start: 0.8288 (t80) cc_final: 0.8085 (t80) REVERT: A 402 MET cc_start: 0.8297 (mtt) cc_final: 0.7849 (mtt) REVERT: A 412 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8486 (p) REVERT: A 481 LEU cc_start: 0.8498 (mm) cc_final: 0.8029 (tp) REVERT: A 510 ASP cc_start: 0.7265 (p0) cc_final: 0.7017 (p0) REVERT: A 528 ASP cc_start: 0.8187 (t0) cc_final: 0.7897 (t0) REVERT: A 565 ASP cc_start: 0.8074 (t0) cc_final: 0.7666 (t70) REVERT: A 663 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7483 (pp) REVERT: 1 56 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8195 (tttp) REVERT: 1 57 ASN cc_start: 0.5440 (p0) cc_final: 0.5068 (p0) REVERT: 1 112 ILE cc_start: 0.8647 (mp) cc_final: 0.8397 (mt) REVERT: 1 165 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8541 (tt) REVERT: 1 209 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: 1 244 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.8331 (t-90) REVERT: 1 253 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8196 (mm-30) REVERT: 1 418 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8632 (ttpt) REVERT: 1 434 GLN cc_start: 0.8485 (mm110) cc_final: 0.8002 (mt0) REVERT: 4 14 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: 2 83 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7329 (tt) REVERT: 2 98 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8209 (tp) REVERT: 3 210 MET cc_start: 0.6964 (mmm) cc_final: 0.6480 (mmt) REVERT: 3 214 ILE cc_start: 0.8211 (tt) cc_final: 0.7982 (tt) REVERT: 3 255 MET cc_start: 0.5726 (tpp) cc_final: 0.5413 (tpt) REVERT: C 97 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7440 (pp20) REVERT: C 109 TYR cc_start: 0.8385 (m-10) cc_final: 0.8161 (m-10) REVERT: C 275 SER cc_start: 0.9169 (m) cc_final: 0.8673 (p) REVERT: B 176 GLU cc_start: 0.7156 (mp0) cc_final: 0.6906 (mt-10) REVERT: B 325 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8601 (pp) outliers start: 81 outliers final: 53 residues processed: 276 average time/residue: 0.1258 time to fit residues: 54.3206 Evaluate side-chains 261 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 56 LYS Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 177 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 209 GLU Chi-restraints excluded: chain 1 residue 220 LEU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 244 HIS Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 27 optimal weight: 0.2980 chunk 136 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 199 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112373 restraints weight = 24015.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111461 restraints weight = 36672.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112678 restraints weight = 34684.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113147 restraints weight = 23442.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113640 restraints weight = 22185.068| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17638 Z= 0.115 Angle : 0.633 10.659 23918 Z= 0.304 Chirality : 0.044 0.362 2688 Planarity : 0.004 0.062 2928 Dihedral : 12.668 162.829 2758 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.09 % Allowed : 17.40 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 2043 helix: 1.54 (0.19), residues: 804 sheet: -0.93 (0.29), residues: 327 loop : -2.60 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 649 TYR 0.022 0.001 TYR 2 41 PHE 0.013 0.001 PHE 1 398 TRP 0.011 0.001 TRP B 299 HIS 0.003 0.000 HIS A 385 Details of bonding type rmsd covalent geometry : bond 0.00249 (17627) covalent geometry : angle 0.61795 (23885) hydrogen bonds : bond 0.04036 ( 627) hydrogen bonds : angle 3.76834 ( 1866) link_BETA1-2 : bond 0.02126 ( 3) link_BETA1-2 : angle 5.15733 ( 9) link_BETA1-4 : bond 0.01155 ( 4) link_BETA1-4 : angle 3.87163 ( 12) link_BETA1-6 : bond 0.00778 ( 1) link_BETA1-6 : angle 2.06528 ( 3) link_NAG-ASN : bond 0.00889 ( 3) link_NAG-ASN : angle 1.78844 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 207 time to evaluate : 0.680 Fit side-chains REVERT: A 122 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: A 204 MET cc_start: 0.8649 (tmm) cc_final: 0.8177 (ttt) REVERT: A 217 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 368 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7553 (t60) REVERT: A 397 TYR cc_start: 0.8328 (t80) cc_final: 0.8096 (t80) REVERT: A 402 MET cc_start: 0.8315 (mtt) cc_final: 0.7886 (mtt) REVERT: A 412 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8498 (p) REVERT: A 481 LEU cc_start: 0.8524 (mm) cc_final: 0.8068 (tp) REVERT: A 510 ASP cc_start: 0.7210 (p0) cc_final: 0.6946 (p0) REVERT: A 528 ASP cc_start: 0.8173 (t0) cc_final: 0.7896 (t0) REVERT: A 565 ASP cc_start: 0.8027 (t0) cc_final: 0.7672 (t70) REVERT: A 663 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7507 (pp) REVERT: 1 56 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8137 (tttp) REVERT: 1 57 ASN cc_start: 0.5323 (p0) cc_final: 0.5047 (p0) REVERT: 1 112 ILE cc_start: 0.8652 (mp) cc_final: 0.8396 (mt) REVERT: 1 165 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8516 (tt) REVERT: 1 244 HIS cc_start: 0.8709 (OUTLIER) cc_final: 0.8323 (t-90) REVERT: 1 250 GLN cc_start: 0.7779 (mt0) cc_final: 0.7531 (mt0) REVERT: 1 434 GLN cc_start: 0.8425 (mm110) cc_final: 0.7972 (mt0) REVERT: 4 14 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: 2 31 LYS cc_start: 0.8536 (ttmm) cc_final: 0.7997 (mtmt) REVERT: 2 83 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7332 (tt) REVERT: 2 98 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8182 (tp) REVERT: 3 210 MET cc_start: 0.6952 (mmm) cc_final: 0.6460 (mmt) REVERT: 3 214 ILE cc_start: 0.8216 (tt) cc_final: 0.7991 (tt) REVERT: 3 255 MET cc_start: 0.5670 (tpp) cc_final: 0.5353 (tpt) REVERT: C 97 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7312 (pp20) REVERT: C 275 SER cc_start: 0.9160 (m) cc_final: 0.8673 (p) REVERT: B 325 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8625 (pp) REVERT: B 415 THR cc_start: 0.9623 (m) cc_final: 0.9163 (p) outliers start: 75 outliers final: 53 residues processed: 267 average time/residue: 0.1208 time to fit residues: 50.8326 Evaluate side-chains 260 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 195 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 56 LYS Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 184 GLU Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 244 HIS Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 1 residue 427 ILE Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 214 TRP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 144 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 ASN ** 1 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 118 GLN C 124 GLN C 224 ASN B 138 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104463 restraints weight = 24270.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104493 restraints weight = 31337.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.105601 restraints weight = 31722.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106327 restraints weight = 19330.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106802 restraints weight = 17489.935| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17638 Z= 0.172 Angle : 0.694 12.119 23918 Z= 0.334 Chirality : 0.046 0.367 2688 Planarity : 0.004 0.065 2928 Dihedral : 12.769 161.279 2755 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.15 % Allowed : 17.95 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 2043 helix: 1.44 (0.19), residues: 808 sheet: -1.11 (0.28), residues: 356 loop : -2.59 (0.18), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.021 0.001 TYR 2 41 PHE 0.020 0.002 PHE C 70 TRP 0.014 0.001 TRP 1 31 HIS 0.003 0.001 HIS 1 416 Details of bonding type rmsd covalent geometry : bond 0.00412 (17627) covalent geometry : angle 0.67985 (23885) hydrogen bonds : bond 0.05388 ( 627) hydrogen bonds : angle 3.95412 ( 1866) link_BETA1-2 : bond 0.02228 ( 3) link_BETA1-2 : angle 5.08832 ( 9) link_BETA1-4 : bond 0.01268 ( 4) link_BETA1-4 : angle 4.16360 ( 12) link_BETA1-6 : bond 0.00589 ( 1) link_BETA1-6 : angle 2.39498 ( 3) link_NAG-ASN : bond 0.00893 ( 3) link_NAG-ASN : angle 1.91865 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 190 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8174 (m-80) REVERT: A 204 MET cc_start: 0.8659 (tmm) cc_final: 0.8171 (ttt) REVERT: A 217 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8185 (tt) REVERT: A 368 TRP cc_start: 0.8055 (OUTLIER) cc_final: 0.7610 (t60) REVERT: A 397 TYR cc_start: 0.8395 (t80) cc_final: 0.8163 (t80) REVERT: A 402 MET cc_start: 0.8273 (mtt) cc_final: 0.7821 (mtt) REVERT: A 412 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 510 ASP cc_start: 0.7416 (p0) cc_final: 0.7164 (p0) REVERT: A 663 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7671 (pp) REVERT: 1 85 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7112 (t80) REVERT: 1 112 ILE cc_start: 0.8650 (mp) cc_final: 0.8403 (mt) REVERT: 1 165 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8584 (tt) REVERT: 1 244 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8348 (t-90) REVERT: 1 418 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8667 (ttpt) REVERT: 1 434 GLN cc_start: 0.8486 (mm110) cc_final: 0.8045 (mt0) REVERT: 4 14 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: 2 98 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8280 (tp) REVERT: 3 210 MET cc_start: 0.6924 (mmm) cc_final: 0.6391 (mmt) REVERT: 3 214 ILE cc_start: 0.8122 (tt) cc_final: 0.7889 (tt) REVERT: 3 255 MET cc_start: 0.5622 (tpp) cc_final: 0.5268 (tpt) REVERT: 3 340 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8270 (p90) REVERT: C 24 ASP cc_start: 0.7077 (p0) cc_final: 0.6644 (p0) REVERT: C 97 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7390 (pp20) REVERT: C 109 TYR cc_start: 0.8339 (m-10) cc_final: 0.8116 (m-10) REVERT: C 275 SER cc_start: 0.9176 (m) cc_final: 0.8670 (p) REVERT: B 176 GLU cc_start: 0.7300 (mp0) cc_final: 0.7067 (mt-10) REVERT: B 325 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8617 (pp) outliers start: 76 outliers final: 56 residues processed: 252 average time/residue: 0.1269 time to fit residues: 50.0241 Evaluate side-chains 251 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 496 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 56 LYS Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 184 GLU Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 220 LEU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 244 HIS Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain 3 residue 340 PHE Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 58 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 118 GLN C 124 GLN C 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103298 restraints weight = 24181.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102547 restraints weight = 30150.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103719 restraints weight = 31849.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104495 restraints weight = 19468.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104922 restraints weight = 17597.407| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17638 Z= 0.191 Angle : 0.704 11.511 23918 Z= 0.341 Chirality : 0.047 0.367 2688 Planarity : 0.004 0.065 2928 Dihedral : 12.809 160.662 2755 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.31 % Allowed : 17.89 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 2043 helix: 1.41 (0.19), residues: 806 sheet: -1.14 (0.28), residues: 356 loop : -2.62 (0.18), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.020 0.001 TYR 2 41 PHE 0.018 0.002 PHE C 70 TRP 0.015 0.001 TRP B 299 HIS 0.003 0.001 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.00460 (17627) covalent geometry : angle 0.68980 (23885) hydrogen bonds : bond 0.05597 ( 627) hydrogen bonds : angle 4.00609 ( 1866) link_BETA1-2 : bond 0.02212 ( 3) link_BETA1-2 : angle 5.12784 ( 9) link_BETA1-4 : bond 0.01225 ( 4) link_BETA1-4 : angle 4.23401 ( 12) link_BETA1-6 : bond 0.00521 ( 1) link_BETA1-6 : angle 2.36177 ( 3) link_NAG-ASN : bond 0.00916 ( 3) link_NAG-ASN : angle 1.93271 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4086 Ramachandran restraints generated. 2043 Oldfield, 0 Emsley, 2043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 188 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 204 MET cc_start: 0.8659 (tmm) cc_final: 0.8176 (ttt) REVERT: A 217 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8186 (tt) REVERT: A 368 TRP cc_start: 0.8056 (OUTLIER) cc_final: 0.7670 (t60) REVERT: A 397 TYR cc_start: 0.8413 (t80) cc_final: 0.8163 (t80) REVERT: A 402 MET cc_start: 0.8313 (mtt) cc_final: 0.7864 (mtt) REVERT: A 412 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 510 ASP cc_start: 0.7430 (p0) cc_final: 0.7186 (p0) REVERT: A 663 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7683 (pp) REVERT: 1 85 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7118 (t80) REVERT: 1 112 ILE cc_start: 0.8633 (mp) cc_final: 0.8387 (mt) REVERT: 1 165 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8606 (tt) REVERT: 1 244 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.8369 (t-90) REVERT: 1 418 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8670 (ttpt) REVERT: 1 434 GLN cc_start: 0.8492 (mm110) cc_final: 0.8065 (mt0) REVERT: 4 14 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: 2 98 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8319 (tp) REVERT: 3 210 MET cc_start: 0.6939 (mmm) cc_final: 0.6402 (mmt) REVERT: 3 214 ILE cc_start: 0.8105 (tt) cc_final: 0.7874 (tt) REVERT: 3 255 MET cc_start: 0.5776 (tpp) cc_final: 0.5358 (tpt) REVERT: 3 340 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8279 (p90) REVERT: C 97 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7490 (pp20) REVERT: C 109 TYR cc_start: 0.8337 (m-10) cc_final: 0.7977 (m-10) REVERT: C 216 ASN cc_start: 0.8497 (t0) cc_final: 0.8297 (t0) REVERT: C 275 SER cc_start: 0.9174 (m) cc_final: 0.8673 (p) REVERT: B 176 GLU cc_start: 0.7353 (mp0) cc_final: 0.7075 (mt-10) REVERT: B 325 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8631 (pp) outliers start: 79 outliers final: 62 residues processed: 251 average time/residue: 0.1217 time to fit residues: 48.0542 Evaluate side-chains 257 residues out of total 1835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 183 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 356 TRP Chi-restraints excluded: chain A residue 368 TRP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 538 TRP Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain 1 residue 50 THR Chi-restraints excluded: chain 1 residue 56 LYS Chi-restraints excluded: chain 1 residue 85 PHE Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 160 THR Chi-restraints excluded: chain 1 residue 165 LEU Chi-restraints excluded: chain 1 residue 180 SER Chi-restraints excluded: chain 1 residue 184 GLU Chi-restraints excluded: chain 1 residue 194 LEU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 1 residue 220 LEU Chi-restraints excluded: chain 1 residue 230 LEU Chi-restraints excluded: chain 1 residue 233 VAL Chi-restraints excluded: chain 1 residue 244 HIS Chi-restraints excluded: chain 1 residue 288 VAL Chi-restraints excluded: chain 1 residue 293 MET Chi-restraints excluded: chain 1 residue 308 VAL Chi-restraints excluded: chain 1 residue 313 THR Chi-restraints excluded: chain 1 residue 342 THR Chi-restraints excluded: chain 1 residue 377 VAL Chi-restraints excluded: chain 1 residue 418 LYS Chi-restraints excluded: chain 1 residue 420 THR Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 4 residue 14 PHE Chi-restraints excluded: chain 4 residue 30 SER Chi-restraints excluded: chain 2 residue 60 ILE Chi-restraints excluded: chain 2 residue 61 GLN Chi-restraints excluded: chain 2 residue 83 ILE Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 3 residue 283 LEU Chi-restraints excluded: chain 3 residue 329 THR Chi-restraints excluded: chain 3 residue 340 PHE Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 214 TRP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 387 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 13 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 17 GLN C 124 GLN C 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106366 restraints weight = 24037.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.105558 restraints weight = 35542.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106812 restraints weight = 32935.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107509 restraints weight = 21826.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107945 restraints weight = 20784.062| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17638 Z= 0.201 Angle : 0.721 11.651 23918 Z= 0.349 Chirality : 0.047 0.364 2688 Planarity : 0.004 0.066 2928 Dihedral : 12.880 159.640 2755 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.31 % Allowed : 17.84 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 2043 helix: 1.35 (0.19), residues: 806 sheet: -1.12 (0.28), residues: 350 loop : -2.66 (0.18), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.020 0.001 TYR 2 41 PHE 0.018 0.002 PHE C 70 TRP 0.016 0.001 TRP B 299 HIS 0.004 0.001 HIS 1 416 Details of bonding type rmsd covalent geometry : bond 0.00486 (17627) covalent geometry : angle 0.70614 (23885) hydrogen bonds : bond 0.05963 ( 627) hydrogen bonds : angle 4.10303 ( 1866) link_BETA1-2 : bond 0.02327 ( 3) link_BETA1-2 : angle 5.15507 ( 9) link_BETA1-4 : bond 0.01332 ( 4) link_BETA1-4 : angle 4.34493 ( 12) link_BETA1-6 : bond 0.00514 ( 1) link_BETA1-6 : angle 2.41121 ( 3) link_NAG-ASN : bond 0.00954 ( 3) link_NAG-ASN : angle 2.04502 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2774.00 seconds wall clock time: 48 minutes 39.15 seconds (2919.15 seconds total)