Starting phenix.real_space_refine on Wed Feb 4 20:54:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yy3_39665/02_2026/8yy3_39665.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yy3_39665/02_2026/8yy3_39665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yy3_39665/02_2026/8yy3_39665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yy3_39665/02_2026/8yy3_39665.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yy3_39665/02_2026/8yy3_39665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yy3_39665/02_2026/8yy3_39665.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 86 5.16 5 C 7915 2.51 5 N 2199 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12668 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3352 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3351 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 406} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2982 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 364} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2895 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'GDP': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.70, per 1000 atoms: 0.21 Number of scatterers: 12668 At special positions: 0 Unit cell: (138.368, 127.84, 119.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 7 15.00 Mg 1 11.99 O 2460 8.00 N 2199 7.00 C 7915 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 553.7 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 15 sheets defined 52.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.543A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 102 through 109 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.457A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.571A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.554A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.735A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.947A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 5.975A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.819A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.787A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.100A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 107 through 126 removed outlier: 4.951A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.874A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.707A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.638A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 removed outlier: 3.514A pdb=" N VAL B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.655A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.803A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.968A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.997A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 426 removed outlier: 3.832A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 347 removed outlier: 3.677A pdb=" N VAL C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 removed outlier: 4.142A pdb=" N ASN C 364 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 392 Processing helix chain 'C' and resid 408 through 424 Proline residue: C 417 - end of helix Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 452 through 469 removed outlier: 3.799A pdb=" N ARG C 456 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 472 No H-bonds generated for 'chain 'C' and resid 470 through 472' Processing helix chain 'C' and resid 524 through 539 Processing helix chain 'C' and resid 592 through 615 removed outlier: 3.742A pdb=" N THR C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 624 removed outlier: 3.704A pdb=" N ASN C 624 " --> pdb=" O PRO C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'C' and resid 625 through 631 Processing helix chain 'C' and resid 631 through 636 Processing helix chain 'C' and resid 650 through 652 No H-bonds generated for 'chain 'C' and resid 650 through 652' Processing helix chain 'C' and resid 653 through 670 removed outlier: 3.838A pdb=" N PHE C 663 " --> pdb=" O LYS C 659 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C 664 " --> pdb=" O SER C 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 347 removed outlier: 3.615A pdb=" N GLU D 334 " --> pdb=" O GLN D 330 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.939A pdb=" N GLU D 363 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 removed outlier: 4.058A pdb=" N SER D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 424 removed outlier: 3.804A pdb=" N ILE D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Proline residue: D 417 - end of helix removed outlier: 3.585A pdb=" N GLN D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 452 through 469 removed outlier: 3.784A pdb=" N ARG D 456 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'D' and resid 524 through 539 Processing helix chain 'D' and resid 549 through 553 removed outlier: 3.839A pdb=" N ARG D 552 " --> pdb=" O ARG D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 615 Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.981A pdb=" N ASN D 624 " --> pdb=" O PRO D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing helix chain 'D' and resid 625 through 631 Processing helix chain 'D' and resid 632 through 636 removed outlier: 3.617A pdb=" N LEU D 635 " --> pdb=" O MET D 632 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY D 636 " --> pdb=" O PRO D 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 632 through 636' Processing helix chain 'D' and resid 653 through 671 removed outlier: 4.003A pdb=" N PHE D 663 " --> pdb=" O LYS D 659 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA D 664 " --> pdb=" O SER D 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.749A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 removed outlier: 4.092A pdb=" N VAL A 62 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.030A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 200 removed outlier: 6.607A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 400 through 401 removed outlier: 4.239A pdb=" N GLN C 400 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS C 353 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG C 350 " --> pdb=" O MET C 643 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 645 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE C 352 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL C 647 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG C 354 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 640 " --> pdb=" O ASN C 427 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 555 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 554 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 400 through 401 removed outlier: 4.239A pdb=" N GLN C 400 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS C 353 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG C 350 " --> pdb=" O MET C 643 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 645 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE C 352 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL C 647 " --> pdb=" O PHE C 352 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG C 354 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 640 " --> pdb=" O ASN C 427 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 555 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 554 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 520 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 371 removed outlier: 3.724A pdb=" N THR C 369 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 381 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 394 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 502 through 504 Processing sheet with id=AB3, first strand: chain 'D' and resid 400 through 402 removed outlier: 6.727A pdb=" N VAL D 351 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE D 402 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N CYS D 353 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 647 " --> pdb=" O ARG D 354 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS D 429 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE D 644 " --> pdb=" O CYS D 429 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE D 431 " --> pdb=" O PHE D 644 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASN D 646 " --> pdb=" O PHE D 431 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR D 433 " --> pdb=" O ASN D 646 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE D 428 " --> pdb=" O ASN D 577 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL D 579 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE D 430 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 581 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA D 432 " --> pdb=" O LEU D 581 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY D 583 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY D 434 " --> pdb=" O GLY D 583 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 400 through 402 removed outlier: 6.727A pdb=" N VAL D 351 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE D 402 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N CYS D 353 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL D 647 " --> pdb=" O ARG D 354 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS D 429 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE D 644 " --> pdb=" O CYS D 429 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE D 431 " --> pdb=" O PHE D 644 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASN D 646 " --> pdb=" O PHE D 431 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR D 433 " --> pdb=" O ASN D 646 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE D 428 " --> pdb=" O ASN D 577 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL D 579 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE D 430 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 581 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA D 432 " --> pdb=" O LEU D 581 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY D 583 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY D 434 " --> pdb=" O GLY D 583 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE D 477 " --> pdb=" O VAL D 522 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 369 through 373 Processing sheet with id=AB6, first strand: chain 'D' and resid 502 through 504 704 hydrogen bonds defined for protein. 2034 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: 2.26 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4241 1.34 - 1.46: 2516 1.46 - 1.58: 6010 1.58 - 1.70: 11 1.70 - 1.81: 136 Bond restraints: 12914 Sorted by residual: bond pdb=" CG LYS D 485 " pdb=" CD LYS D 485 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.78e+00 bond pdb=" CZ ARG D 549 " pdb=" NH1 ARG D 549 " ideal model delta sigma weight residual 1.323 1.293 0.030 1.40e-02 5.10e+03 4.75e+00 bond pdb=" C5 GDP B 502 " pdb=" C4 GDP B 502 " ideal model delta sigma weight residual 1.490 1.456 0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C HIS B 105 " pdb=" N TYR B 106 " ideal model delta sigma weight residual 1.332 1.309 0.024 1.40e-02 5.10e+03 2.83e+00 bond pdb=" CG1 ILE D 484 " pdb=" CD1 ILE D 484 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.77e+00 ... (remaining 12909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 17143 1.89 - 3.77: 288 3.77 - 5.66: 51 5.66 - 7.54: 14 7.54 - 9.43: 2 Bond angle restraints: 17498 Sorted by residual: angle pdb=" C HIS B 105 " pdb=" N TYR B 106 " pdb=" CA TYR B 106 " ideal model delta sigma weight residual 121.54 115.15 6.39 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C SER B 115 " pdb=" N VAL B 116 " pdb=" CA VAL B 116 " ideal model delta sigma weight residual 122.35 118.70 3.65 1.18e+00 7.18e-01 9.57e+00 angle pdb=" CG LYS D 485 " pdb=" CD LYS D 485 " pdb=" CE LYS D 485 " ideal model delta sigma weight residual 111.30 104.84 6.46 2.30e+00 1.89e-01 7.88e+00 angle pdb=" C TRP B 21 " pdb=" N GLU B 22 " pdb=" CA GLU B 22 " ideal model delta sigma weight residual 120.29 116.37 3.92 1.42e+00 4.96e-01 7.61e+00 angle pdb=" CA LEU D 482 " pdb=" CB LEU D 482 " pdb=" CG LEU D 482 " ideal model delta sigma weight residual 116.30 125.73 -9.43 3.50e+00 8.16e-02 7.26e+00 ... (remaining 17493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 7570 31.66 - 63.31: 203 63.31 - 94.97: 24 94.97 - 126.62: 2 126.62 - 158.28: 1 Dihedral angle restraints: 7800 sinusoidal: 3158 harmonic: 4642 Sorted by residual: dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -53.69 158.28 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -173.24 -117.49 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" O3B GTP B 501 " pdb=" O3A GTP B 501 " pdb=" PB GTP B 501 " pdb=" PA GTP B 501 " ideal model delta sinusoidal sigma weight residual -68.92 -174.29 105.37 1 2.00e+01 2.50e-03 3.04e+01 ... (remaining 7797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1103 0.029 - 0.057: 490 0.057 - 0.086: 203 0.086 - 0.114: 130 0.114 - 0.143: 26 Chirality restraints: 1952 Sorted by residual: chirality pdb=" C3' GTP B 501 " pdb=" C2' GTP B 501 " pdb=" C4' GTP B 501 " pdb=" O3' GTP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.61 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA MET C 632 " pdb=" N MET C 632 " pdb=" C MET C 632 " pdb=" CB MET C 632 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" C2' GTP B 501 " pdb=" C1' GTP B 501 " pdb=" C3' GTP B 501 " pdb=" O2' GTP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.61 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1949 not shown) Planarity restraints: 2273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 641 " 0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C THR C 641 " -0.072 2.00e-02 2.50e+03 pdb=" O THR C 641 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU C 642 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 181 " 0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO B 182 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 260 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C VAL A 260 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 260 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 261 " 0.011 2.00e-02 2.50e+03 ... (remaining 2270 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 222 2.58 - 3.16: 11792 3.16 - 3.74: 21237 3.74 - 4.32: 29077 4.32 - 4.90: 46498 Nonbonded interactions: 108826 Sorted by model distance: nonbonded pdb=" O THR A 381 " pdb=" OH TYR A 432 " model vdw 2.004 3.040 nonbonded pdb="MG MG D 801 " pdb=" O3B ADP D 802 " model vdw 2.046 2.170 nonbonded pdb=" OG SER B 145 " pdb=" OG SER B 188 " model vdw 2.060 3.040 nonbonded pdb=" OD1 ASN A 101 " pdb=" NZ LYS B 252 " model vdw 2.107 3.120 nonbonded pdb=" O LYS D 659 " pdb=" NH1 ARG D 662 " model vdw 2.124 3.120 ... (remaining 108821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 296 through 587 or resid 599 through 617 or (resid 618 and \ (name N or name CA or name C or name O or name CB )) or resid 619 through 670)) \ selection = (chain 'D' and (resid 296 through 308 or (resid 309 and (name N or name CA or na \ me C or name O or name CB )) or resid 310 through 670)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.390 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.810 Find NCS groups from input model: 0.200 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4790 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 : 0.010 0.890 12917 Z= 0.834 Angle : 0.663 9.429 17498 Z= 0.343 Chirality : 0.044 0.143 1952 Planarity : 0.005 0.061 2273 Dihedral : 14.262 158.279 4800 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.87 % Allowed : 8.47 % Favored : 88.66 % 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: 0.12 (0.21), residues: 1584 helix: 0.96 (0.19), residues: 709 sheet: -0.03 (0.34), residues: 269 loop : -0.83 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 380 TYR 0.013 0.001 TYR A 172 PHE 0.016 0.002 PHE C 663 TRP 0.013 0.001 TRP A 21 HIS 0.006 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00607 (12914) covalent geometry : angle 0.66335 (17498) hydrogen bonds : bond 0.16438 ( 650) hydrogen bonds : angle 7.14057 ( 2034) Misc. bond : bond 0.51370 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 430 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 CYS cc_start: 0.6016 (t) cc_final: 0.5789 (t) REVERT: A 60 LYS cc_start: 0.3655 (ttpt) cc_final: 0.3225 (mmmt) REVERT: A 80 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7398 (p) REVERT: A 87 PHE cc_start: 0.8637 (m-80) cc_final: 0.8339 (m-80) REVERT: A 115 ILE cc_start: 0.6887 (tt) cc_final: 0.6465 (tp) REVERT: A 125 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7394 (mm) REVERT: A 129 CYS cc_start: 0.4425 (t) cc_final: 0.4181 (m) REVERT: A 220 GLU cc_start: 0.7754 (pm20) cc_final: 0.7514 (pm20) REVERT: A 276 ILE cc_start: 0.7694 (pt) cc_final: 0.7317 (pt) REVERT: A 352 LYS cc_start: 0.3042 (mmtt) cc_final: 0.2123 (mmtt) REVERT: A 375 VAL cc_start: 0.7555 (p) cc_final: 0.7286 (p) REVERT: A 413 MET cc_start: 0.7590 (mpp) cc_final: 0.7300 (mpp) REVERT: B 155 ILE cc_start: 0.6691 (mm) cc_final: 0.5979 (mm) REVERT: B 156 ARG cc_start: 0.7308 (tpp80) cc_final: 0.6963 (tpp80) REVERT: B 163 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7658 (pt) REVERT: B 164 MET cc_start: 0.6092 (mmm) cc_final: 0.5465 (mmm) REVERT: B 212 PHE cc_start: 0.8553 (t80) cc_final: 0.8255 (t80) REVERT: B 267 MET cc_start: 0.6341 (mtp) cc_final: 0.6073 (mtm) REVERT: B 324 LYS cc_start: 0.8059 (tptt) cc_final: 0.7753 (tptm) REVERT: B 327 ASP cc_start: 0.8267 (m-30) cc_final: 0.8027 (m-30) REVERT: B 328 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: B 331 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8256 (tt) REVERT: B 337 ASN cc_start: 0.8701 (m110) cc_final: 0.8306 (m-40) REVERT: C 378 VAL cc_start: 0.3168 (p) cc_final: 0.2931 (p) REVERT: C 411 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6953 (mt) REVERT: C 414 MET cc_start: 0.8073 (mmp) cc_final: 0.7797 (mmp) REVERT: C 444 MET cc_start: 0.7625 (mmp) cc_final: 0.7224 (mmp) REVERT: C 459 ASP cc_start: 0.8413 (m-30) cc_final: 0.7723 (p0) REVERT: C 500 MET cc_start: 0.5803 (mmt) cc_final: 0.3986 (mmt) REVERT: C 517 ILE cc_start: 0.7685 (pt) cc_final: 0.7331 (tp) REVERT: C 541 THR cc_start: 0.1345 (OUTLIER) cc_final: 0.1020 (m) REVERT: C 593 MET cc_start: 0.3450 (ptm) cc_final: 0.3234 (ptp) REVERT: C 601 ARG cc_start: 0.4101 (mtp85) cc_final: 0.3299 (ptp-110) REVERT: C 620 ILE cc_start: 0.8210 (mt) cc_final: 0.7923 (mp) REVERT: C 622 TYR cc_start: 0.7519 (m-80) cc_final: 0.6537 (m-80) REVERT: C 632 MET cc_start: 0.6298 (ptm) cc_final: 0.5413 (ptt) REVERT: C 655 GLN cc_start: 0.5497 (pm20) cc_final: 0.4793 (pm20) REVERT: C 660 SER cc_start: 0.4338 (OUTLIER) cc_final: 0.3999 (m) REVERT: D 366 MET cc_start: -0.1636 (tpt) cc_final: -0.3823 (mtt) REVERT: D 391 MET cc_start: 0.2851 (ptp) cc_final: 0.2433 (ptp) REVERT: D 421 SER cc_start: 0.0609 (m) cc_final: -0.0198 (t) REVERT: D 504 MET cc_start: 0.0974 (mpp) cc_final: 0.0261 (ptt) REVERT: D 532 MET cc_start: -0.1146 (mtp) cc_final: -0.1356 (mtt) REVERT: D 632 MET cc_start: -0.0174 (tmm) cc_final: -0.1178 (mmm) outliers start: 40 outliers final: 11 residues processed: 453 average time/residue: 0.1051 time to fit residues: 67.9435 Evaluate side-chains 272 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain D residue 537 MET Chi-restraints excluded: chain D residue 662 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 256 GLN A 406 HIS B 105 HIS B 245 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS C 305 GLN C 317 GLN C 339 HIS C 400 GLN C 508 ASN ** C 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 600 ASN ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 638 ASN ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN D 420 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.231005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.140998 restraints weight = 19584.645| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 8.37 r_work: 0.3359 rms_B_bonded: 6.58 restraints_weight: 2.0000 r_work: 0.3499 rms_B_bonded: 5.12 restraints_weight: 4.0000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12917 Z= 0.250 Angle : 0.772 14.546 17498 Z= 0.393 Chirality : 0.051 0.299 1952 Planarity : 0.006 0.057 2273 Dihedral : 9.087 156.510 1796 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.30 % Allowed : 15.00 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1584 helix: 0.74 (0.18), residues: 727 sheet: 0.22 (0.34), residues: 257 loop : -1.11 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 422 TYR 0.019 0.002 TYR B 310 PHE 0.018 0.002 PHE B 167 TRP 0.020 0.002 TRP A 21 HIS 0.009 0.002 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00553 (12914) covalent geometry : angle 0.77188 (17498) hydrogen bonds : bond 0.04891 ( 650) hydrogen bonds : angle 5.38781 ( 2034) Misc. bond : bond 0.00404 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.3932 (ttpt) cc_final: 0.2893 (mmmt) REVERT: A 300 ASN cc_start: 0.9131 (t0) cc_final: 0.8754 (t0) REVERT: A 352 LYS cc_start: 0.5126 (mmtt) cc_final: 0.3987 (mmtt) REVERT: A 381 THR cc_start: 0.8379 (p) cc_final: 0.8088 (p) REVERT: A 422 ARG cc_start: 0.8080 (tpt90) cc_final: 0.7801 (tpt90) REVERT: A 430 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8527 (pttm) REVERT: B 222 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8457 (m-80) REVERT: B 245 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8644 (mm-40) REVERT: B 379 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8403 (mtmt) REVERT: B 415 MET cc_start: 0.6899 (mtm) cc_final: 0.6617 (mtm) REVERT: C 402 PHE cc_start: 0.7550 (m-80) cc_final: 0.7301 (m-80) REVERT: C 444 MET cc_start: 0.7841 (mmp) cc_final: 0.7426 (mmp) REVERT: C 500 MET cc_start: 0.3057 (mmt) cc_final: 0.2433 (mmt) REVERT: C 517 ILE cc_start: 0.6190 (pt) cc_final: 0.5606 (pt) REVERT: C 601 ARG cc_start: 0.5946 (mtp85) cc_final: 0.5468 (mtp85) REVERT: C 622 TYR cc_start: 0.6365 (m-80) cc_final: 0.5551 (m-80) REVERT: C 632 MET cc_start: 0.5036 (ptm) cc_final: 0.4520 (ptm) REVERT: D 340 ASN cc_start: 0.6271 (p0) cc_final: 0.5065 (m-40) outliers start: 46 outliers final: 25 residues processed: 287 average time/residue: 0.1225 time to fit residues: 49.2395 Evaluate side-chains 232 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain D residue 533 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 29 optimal weight: 7.9990 chunk 149 optimal weight: 30.0000 chunk 139 optimal weight: 50.0000 chunk 142 optimal weight: 50.0000 chunk 15 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 150 optimal weight: 40.0000 chunk 17 optimal weight: 4.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN C 420 GLN C 565 HIS ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 GLN C 668 ASN D 314 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.227578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135172 restraints weight = 19437.891| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 7.45 r_work: 0.3270 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12917 Z= 0.218 Angle : 0.705 7.979 17498 Z= 0.360 Chirality : 0.049 0.185 1952 Planarity : 0.005 0.058 2273 Dihedral : 8.509 160.360 1770 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.88 % Allowed : 16.65 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.21), residues: 1584 helix: 0.87 (0.19), residues: 714 sheet: 0.37 (0.34), residues: 250 loop : -1.12 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 335 TYR 0.018 0.002 TYR A 224 PHE 0.023 0.002 PHE C 644 TRP 0.014 0.001 TRP A 21 HIS 0.009 0.001 HIS D 629 Details of bonding type rmsd covalent geometry : bond 0.00495 (12914) covalent geometry : angle 0.70478 (17498) hydrogen bonds : bond 0.04872 ( 650) hydrogen bonds : angle 5.02803 ( 2034) Misc. bond : bond 0.00191 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.4640 (mmt180) cc_final: 0.4410 (mmt180) REVERT: A 60 LYS cc_start: 0.4279 (ttpt) cc_final: 0.2570 (tptm) REVERT: A 112 LYS cc_start: 0.9131 (ptpp) cc_final: 0.8668 (pttp) REVERT: A 128 GLN cc_start: 0.8759 (tp40) cc_final: 0.8422 (tm-30) REVERT: A 168 GLU cc_start: 0.8726 (mp0) cc_final: 0.8516 (mp0) REVERT: A 172 TYR cc_start: 0.8641 (t80) cc_final: 0.8394 (t80) REVERT: A 224 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.8347 (m-10) REVERT: A 297 GLU cc_start: 0.8868 (pt0) cc_final: 0.8385 (pt0) REVERT: A 302 MET cc_start: 0.8826 (ttm) cc_final: 0.8556 (mtt) REVERT: A 351 PHE cc_start: 0.8579 (m-80) cc_final: 0.8344 (m-80) REVERT: A 352 LYS cc_start: 0.5536 (mmtt) cc_final: 0.3562 (mmtp) REVERT: A 425 MET cc_start: 0.8895 (mmp) cc_final: 0.8592 (mmp) REVERT: A 430 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8579 (pttm) REVERT: B 245 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8734 (mm-40) REVERT: C 414 MET cc_start: 0.8134 (mmp) cc_final: 0.7890 (mmp) REVERT: C 444 MET cc_start: 0.7945 (mmp) cc_final: 0.7623 (mmp) REVERT: C 614 LEU cc_start: 0.6957 (mt) cc_final: 0.6294 (mt) REVERT: C 615 GLN cc_start: 0.8394 (mt0) cc_final: 0.8040 (mm-40) REVERT: C 620 ILE cc_start: 0.7370 (mt) cc_final: 0.6981 (mp) REVERT: C 622 TYR cc_start: 0.6439 (m-80) cc_final: 0.5803 (m-80) REVERT: C 632 MET cc_start: 0.5037 (ptm) cc_final: 0.4556 (ptm) REVERT: D 623 ARG cc_start: 0.3602 (mtm-85) cc_final: 0.3343 (ptt-90) outliers start: 54 outliers final: 26 residues processed: 254 average time/residue: 0.1086 time to fit residues: 39.0484 Evaluate side-chains 205 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 533 HIS Chi-restraints excluded: chain D residue 537 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 22 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 113 optimal weight: 40.0000 chunk 28 optimal weight: 0.9990 chunk 143 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 347 ASN C 646 ASN C 668 ASN D 314 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS D 608 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.227862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138410 restraints weight = 19148.490| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 7.32 r_work: 0.3221 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.6628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12917 Z= 0.186 Angle : 0.655 8.717 17498 Z= 0.331 Chirality : 0.047 0.168 1952 Planarity : 0.005 0.051 2273 Dihedral : 8.367 158.959 1770 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.45 % Allowed : 17.80 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1584 helix: 0.97 (0.19), residues: 713 sheet: 0.10 (0.33), residues: 266 loop : -0.97 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 318 TYR 0.014 0.001 TYR A 357 PHE 0.019 0.002 PHE D 352 TRP 0.015 0.002 TRP A 21 HIS 0.004 0.001 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.00426 (12914) covalent geometry : angle 0.65541 (17498) hydrogen bonds : bond 0.04385 ( 650) hydrogen bonds : angle 4.89455 ( 2034) Misc. bond : bond 0.00143 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.3978 (ttpt) cc_final: 0.2512 (tptm) REVERT: A 112 LYS cc_start: 0.9097 (ptpp) cc_final: 0.8705 (pttp) REVERT: A 123 ARG cc_start: 0.8802 (tmm-80) cc_final: 0.8400 (tpp-160) REVERT: A 128 GLN cc_start: 0.8767 (tp40) cc_final: 0.8397 (tm-30) REVERT: A 224 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.7949 (m-10) REVERT: A 352 LYS cc_start: 0.5413 (mmtt) cc_final: 0.3382 (mmtp) REVERT: A 425 MET cc_start: 0.8893 (mmp) cc_final: 0.8547 (mmp) REVERT: A 430 LYS cc_start: 0.9047 (ttpp) cc_final: 0.8632 (pttm) REVERT: A 432 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 284 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8486 (pp) REVERT: B 362 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8495 (ptmm) REVERT: C 414 MET cc_start: 0.8159 (mmp) cc_final: 0.7904 (mmp) REVERT: C 444 MET cc_start: 0.8145 (mmp) cc_final: 0.7759 (mmp) REVERT: C 614 LEU cc_start: 0.7002 (mt) cc_final: 0.6417 (mt) REVERT: C 615 GLN cc_start: 0.8372 (mt0) cc_final: 0.8067 (mm-40) REVERT: C 620 ILE cc_start: 0.7412 (mt) cc_final: 0.7171 (mp) REVERT: C 622 TYR cc_start: 0.6243 (m-80) cc_final: 0.5665 (m-80) REVERT: C 632 MET cc_start: 0.5239 (ptm) cc_final: 0.4836 (ptm) REVERT: C 655 GLN cc_start: 0.5702 (pm20) cc_final: 0.5335 (pm20) REVERT: D 623 ARG cc_start: 0.3503 (mtm-85) cc_final: 0.3288 (ptt-90) outliers start: 48 outliers final: 30 residues processed: 231 average time/residue: 0.1202 time to fit residues: 39.6662 Evaluate side-chains 208 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 454 ILE Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 533 HIS Chi-restraints excluded: chain D residue 562 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 56 optimal weight: 9.9990 chunk 156 optimal weight: 50.0000 chunk 131 optimal weight: 50.0000 chunk 86 optimal weight: 50.0000 chunk 117 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 332 ASN ** C 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 GLN C 668 ASN D 317 GLN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.226324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.141897 restraints weight = 19264.059| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 5.93 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12917 Z= 0.193 Angle : 0.665 8.714 17498 Z= 0.338 Chirality : 0.047 0.231 1952 Planarity : 0.005 0.051 2273 Dihedral : 8.333 159.494 1770 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.37 % Allowed : 19.31 % Favored : 77.32 % 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: 0.12 (0.21), residues: 1584 helix: 0.97 (0.19), residues: 716 sheet: 0.18 (0.33), residues: 256 loop : -0.99 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 335 TYR 0.015 0.001 TYR C 433 PHE 0.017 0.002 PHE D 352 TRP 0.013 0.001 TRP A 21 HIS 0.022 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00437 (12914) covalent geometry : angle 0.66511 (17498) hydrogen bonds : bond 0.04395 ( 650) hydrogen bonds : angle 4.87184 ( 2034) Misc. bond : bond 0.00143 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.3406 (ttpt) cc_final: 0.2642 (tptm) REVERT: A 112 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8262 (pttm) REVERT: A 128 GLN cc_start: 0.8376 (tp40) cc_final: 0.8114 (tm-30) REVERT: A 168 GLU cc_start: 0.8089 (mp0) cc_final: 0.7552 (mp0) REVERT: A 177 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7710 (p) REVERT: A 224 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: A 290 GLU cc_start: 0.8081 (pp20) cc_final: 0.7804 (pp20) REVERT: A 352 LYS cc_start: 0.4755 (mmtt) cc_final: 0.3673 (mmtp) REVERT: A 377 MET cc_start: 0.8654 (ttt) cc_final: 0.8339 (ttt) REVERT: A 425 MET cc_start: 0.8811 (mmp) cc_final: 0.8584 (mmm) REVERT: A 430 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8476 (pttm) REVERT: A 432 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7353 (t80) REVERT: B 245 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8230 (mt0) REVERT: B 284 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8177 (pp) REVERT: B 323 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6643 (mtp) REVERT: B 363 MET cc_start: 0.8149 (mtp) cc_final: 0.7797 (mtp) REVERT: C 414 MET cc_start: 0.8175 (mmp) cc_final: 0.7777 (mmp) REVERT: C 444 MET cc_start: 0.8219 (mmp) cc_final: 0.7833 (mmp) REVERT: C 622 TYR cc_start: 0.6848 (m-80) cc_final: 0.6091 (m-80) REVERT: C 631 LEU cc_start: 0.8028 (mt) cc_final: 0.7823 (mt) REVERT: C 632 MET cc_start: 0.5452 (ptm) cc_final: 0.4964 (ptm) REVERT: D 623 ARG cc_start: 0.3477 (mtm-85) cc_final: 0.3069 (ptt-90) outliers start: 47 outliers final: 29 residues processed: 216 average time/residue: 0.1039 time to fit residues: 32.6647 Evaluate side-chains 202 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 562 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 124 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 chunk 72 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 118 optimal weight: 50.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 668 ASN D 314 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS D 608 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.226438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138000 restraints weight = 19098.010| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 6.84 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12917 Z= 0.169 Angle : 0.635 8.735 17498 Z= 0.323 Chirality : 0.046 0.205 1952 Planarity : 0.005 0.051 2273 Dihedral : 8.250 158.911 1770 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.80 % Allowed : 19.31 % Favored : 76.88 % 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: 0.12 (0.21), residues: 1584 helix: 1.00 (0.19), residues: 716 sheet: 0.11 (0.33), residues: 261 loop : -0.97 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 318 TYR 0.016 0.001 TYR C 433 PHE 0.019 0.001 PHE A 169 TRP 0.013 0.001 TRP A 21 HIS 0.013 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00381 (12914) covalent geometry : angle 0.63489 (17498) hydrogen bonds : bond 0.04249 ( 650) hydrogen bonds : angle 4.77519 ( 2034) Misc. bond : bond 0.00101 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.3405 (ttpt) cc_final: 0.2696 (tptm) REVERT: A 128 GLN cc_start: 0.8432 (tp40) cc_final: 0.8158 (tm-30) REVERT: A 163 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7834 (pttm) REVERT: A 205 ASP cc_start: 0.7844 (t0) cc_final: 0.7362 (m-30) REVERT: A 224 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: A 351 PHE cc_start: 0.8304 (m-80) cc_final: 0.8021 (m-80) REVERT: A 352 LYS cc_start: 0.4735 (mmtt) cc_final: 0.3374 (mmtm) REVERT: A 377 MET cc_start: 0.8611 (ttt) cc_final: 0.8335 (ttt) REVERT: A 425 MET cc_start: 0.8761 (mmp) cc_final: 0.8554 (mmm) REVERT: A 432 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 228 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8912 (mp) REVERT: B 245 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8167 (mt0) REVERT: B 323 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.6316 (mtp) REVERT: C 414 MET cc_start: 0.8160 (mmp) cc_final: 0.7753 (mmp) REVERT: C 444 MET cc_start: 0.8273 (mmp) cc_final: 0.7903 (mmp) REVERT: C 622 TYR cc_start: 0.6897 (m-80) cc_final: 0.6158 (m-80) REVERT: C 631 LEU cc_start: 0.8032 (mt) cc_final: 0.7813 (mt) REVERT: C 632 MET cc_start: 0.5351 (ptm) cc_final: 0.4894 (ptm) REVERT: D 623 ARG cc_start: 0.3333 (mtm-85) cc_final: 0.2981 (ptt-90) outliers start: 53 outliers final: 37 residues processed: 211 average time/residue: 0.1145 time to fit residues: 35.1603 Evaluate side-chains 200 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 533 HIS Chi-restraints excluded: chain D residue 562 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 30 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 143 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN D 314 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.226702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143984 restraints weight = 19092.252| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 4.11 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12917 Z= 0.174 Angle : 0.645 9.640 17498 Z= 0.328 Chirality : 0.046 0.192 1952 Planarity : 0.004 0.053 2273 Dihedral : 8.186 158.814 1769 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.73 % Allowed : 18.66 % Favored : 77.60 % 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: 0.07 (0.21), residues: 1584 helix: 0.92 (0.18), residues: 717 sheet: 0.14 (0.33), residues: 263 loop : -0.98 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 318 TYR 0.017 0.001 TYR C 433 PHE 0.025 0.002 PHE A 169 TRP 0.012 0.001 TRP A 21 HIS 0.011 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00397 (12914) covalent geometry : angle 0.64490 (17498) hydrogen bonds : bond 0.04245 ( 650) hydrogen bonds : angle 4.77176 ( 2034) Misc. bond : bond 0.00102 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 162 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.3415 (ttpt) cc_final: 0.2768 (tptm) REVERT: A 163 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7850 (pttm) REVERT: A 168 GLU cc_start: 0.8003 (mp0) cc_final: 0.7692 (mp0) REVERT: A 224 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: A 351 PHE cc_start: 0.8232 (m-80) cc_final: 0.8014 (m-80) REVERT: A 352 LYS cc_start: 0.4780 (mmtt) cc_final: 0.3287 (mmtm) REVERT: A 377 MET cc_start: 0.8766 (ttt) cc_final: 0.8490 (ttt) REVERT: A 425 MET cc_start: 0.8644 (mmp) cc_final: 0.8439 (mmm) REVERT: A 432 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7200 (t80) REVERT: B 228 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8959 (mp) REVERT: B 245 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8252 (mt0) REVERT: B 323 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6505 (mtp) REVERT: B 388 MET cc_start: 0.3447 (mmt) cc_final: 0.2665 (mmt) REVERT: C 414 MET cc_start: 0.7995 (mmp) cc_final: 0.7551 (mmp) REVERT: C 444 MET cc_start: 0.8280 (mmp) cc_final: 0.7776 (mmp) REVERT: C 529 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7530 (mmt90) REVERT: C 622 TYR cc_start: 0.7862 (m-80) cc_final: 0.6976 (m-80) REVERT: C 632 MET cc_start: 0.6071 (ptm) cc_final: 0.5526 (ptm) outliers start: 52 outliers final: 36 residues processed: 197 average time/residue: 0.1159 time to fit residues: 33.5748 Evaluate side-chains 198 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 412 PHE Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 562 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 4 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 109 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 668 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.228153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.145562 restraints weight = 18735.120| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 4.19 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.7634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12917 Z= 0.154 Angle : 0.652 11.383 17498 Z= 0.330 Chirality : 0.046 0.190 1952 Planarity : 0.004 0.053 2273 Dihedral : 8.125 158.146 1767 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.59 % Allowed : 19.31 % Favored : 77.10 % 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: 0.09 (0.21), residues: 1584 helix: 0.90 (0.18), residues: 716 sheet: 0.17 (0.33), residues: 263 loop : -0.94 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 503 TYR 0.017 0.001 TYR C 433 PHE 0.020 0.001 PHE A 169 TRP 0.013 0.001 TRP A 21 HIS 0.010 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00349 (12914) covalent geometry : angle 0.65176 (17498) hydrogen bonds : bond 0.04163 ( 650) hydrogen bonds : angle 4.77176 ( 2034) Misc. bond : bond 0.00094 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.3458 (ttpt) cc_final: 0.2839 (tptm) REVERT: A 113 GLU cc_start: 0.7819 (mp0) cc_final: 0.7590 (mp0) REVERT: A 168 GLU cc_start: 0.7994 (mp0) cc_final: 0.7668 (mp0) REVERT: A 205 ASP cc_start: 0.7711 (t0) cc_final: 0.7316 (m-30) REVERT: A 224 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: A 352 LYS cc_start: 0.4698 (mmtt) cc_final: 0.3270 (mmtm) REVERT: A 377 MET cc_start: 0.8779 (ttt) cc_final: 0.8456 (ttt) REVERT: A 432 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7047 (t80) REVERT: B 323 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6189 (mtp) REVERT: B 388 MET cc_start: 0.3333 (mmt) cc_final: 0.2575 (mmt) REVERT: B 424 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: C 414 MET cc_start: 0.8025 (mmp) cc_final: 0.7565 (mmp) REVERT: C 444 MET cc_start: 0.8235 (mmp) cc_final: 0.7719 (mmp) REVERT: C 529 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7583 (mmt90) REVERT: C 622 TYR cc_start: 0.7729 (m-80) cc_final: 0.6891 (m-80) REVERT: C 632 MET cc_start: 0.6032 (ptm) cc_final: 0.5516 (ptm) outliers start: 50 outliers final: 37 residues processed: 194 average time/residue: 0.1082 time to fit residues: 30.5378 Evaluate side-chains 191 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 562 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 103 optimal weight: 6.9990 chunk 106 optimal weight: 30.0000 chunk 17 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 137 optimal weight: 40.0000 chunk 156 optimal weight: 20.0000 chunk 20 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN C 668 ASN ** D 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.225684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138206 restraints weight = 19111.060| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 5.84 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12917 Z= 0.170 Angle : 0.674 11.130 17498 Z= 0.341 Chirality : 0.047 0.193 1952 Planarity : 0.004 0.053 2273 Dihedral : 8.138 158.258 1767 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.30 % Allowed : 19.89 % Favored : 76.81 % 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: 0.07 (0.21), residues: 1584 helix: 0.87 (0.18), residues: 716 sheet: 0.11 (0.33), residues: 263 loop : -0.90 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 503 TYR 0.013 0.001 TYR A 224 PHE 0.024 0.002 PHE A 169 TRP 0.012 0.001 TRP A 21 HIS 0.010 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00386 (12914) covalent geometry : angle 0.67447 (17498) hydrogen bonds : bond 0.04233 ( 650) hydrogen bonds : angle 4.80058 ( 2034) Misc. bond : bond 0.00103 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.3531 (ttpt) cc_final: 0.2928 (tptm) REVERT: A 205 ASP cc_start: 0.7896 (t0) cc_final: 0.7487 (m-30) REVERT: A 224 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: A 352 LYS cc_start: 0.4720 (mmtt) cc_final: 0.3277 (mmtm) REVERT: A 377 MET cc_start: 0.8634 (ttt) cc_final: 0.8322 (ttt) REVERT: A 432 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7174 (t80) REVERT: B 323 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6264 (mtp) REVERT: B 388 MET cc_start: 0.3297 (mmt) cc_final: 0.2591 (mmt) REVERT: B 424 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: C 414 MET cc_start: 0.8078 (mmp) cc_final: 0.7657 (mmp) REVERT: C 444 MET cc_start: 0.8242 (mmp) cc_final: 0.7824 (mmp) REVERT: C 529 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7566 (mmt90) REVERT: C 622 TYR cc_start: 0.7144 (m-80) cc_final: 0.6483 (m-80) outliers start: 46 outliers final: 36 residues processed: 189 average time/residue: 0.1095 time to fit residues: 30.0163 Evaluate side-chains 194 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 481 PHE Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 562 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 65 optimal weight: 1.9990 chunk 151 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 84 optimal weight: 50.0000 chunk 100 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 668 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.224912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133554 restraints weight = 19117.523| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.61 r_work: 0.3244 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.7930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12917 Z= 0.189 Angle : 0.686 10.869 17498 Z= 0.349 Chirality : 0.047 0.194 1952 Planarity : 0.005 0.053 2273 Dihedral : 8.211 159.283 1767 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.94 % Allowed : 20.32 % Favored : 76.74 % 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: 0.02 (0.21), residues: 1584 helix: 0.84 (0.19), residues: 716 sheet: 0.10 (0.33), residues: 263 loop : -0.95 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 503 TYR 0.014 0.001 TYR C 433 PHE 0.035 0.002 PHE C 396 TRP 0.011 0.001 TRP A 21 HIS 0.010 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00436 (12914) covalent geometry : angle 0.68591 (17498) hydrogen bonds : bond 0.04379 ( 650) hydrogen bonds : angle 4.81723 ( 2034) Misc. bond : bond 0.00100 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.3976 (ttpt) cc_final: 0.2785 (tptm) REVERT: A 205 ASP cc_start: 0.8100 (t0) cc_final: 0.7653 (m-30) REVERT: A 224 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: A 313 MET cc_start: 0.8279 (mmt) cc_final: 0.8006 (mmt) REVERT: A 352 LYS cc_start: 0.5469 (mmtt) cc_final: 0.3568 (mmtm) REVERT: A 357 TYR cc_start: 0.7935 (p90) cc_final: 0.7291 (p90) REVERT: A 432 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.6875 (t80) REVERT: B 323 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.6735 (mtp) REVERT: B 388 MET cc_start: 0.4337 (mmt) cc_final: 0.3227 (mmt) REVERT: C 414 MET cc_start: 0.8132 (mmp) cc_final: 0.7823 (mmp) REVERT: C 444 MET cc_start: 0.8271 (mmp) cc_final: 0.7967 (mmp) REVERT: C 503 ARG cc_start: 0.6396 (tpp80) cc_final: 0.5930 (tpp-160) REVERT: C 529 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7604 (mmt90) REVERT: C 532 MET cc_start: 0.7630 (mtm) cc_final: 0.7384 (mtm) REVERT: C 622 TYR cc_start: 0.6464 (m-80) cc_final: 0.6054 (m-80) outliers start: 41 outliers final: 34 residues processed: 185 average time/residue: 0.1188 time to fit residues: 31.7337 Evaluate side-chains 190 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 470 ASN Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 562 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 50.0000 chunk 138 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 103 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.226667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139823 restraints weight = 19455.590| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.73 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.8046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12917 Z= 0.155 Angle : 0.663 10.941 17498 Z= 0.336 Chirality : 0.046 0.181 1952 Planarity : 0.004 0.053 2273 Dihedral : 8.150 158.608 1767 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.94 % Allowed : 20.82 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1584 helix: 0.98 (0.19), residues: 710 sheet: 0.17 (0.33), residues: 262 loop : -0.87 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 503 TYR 0.013 0.001 TYR A 224 PHE 0.037 0.002 PHE C 396 TRP 0.013 0.001 TRP A 21 HIS 0.008 0.001 HIS C 339 Details of bonding type rmsd covalent geometry : bond 0.00353 (12914) covalent geometry : angle 0.66250 (17498) hydrogen bonds : bond 0.04107 ( 650) hydrogen bonds : angle 4.75955 ( 2034) Misc. bond : bond 0.00099 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5085.94 seconds wall clock time: 87 minutes 30.32 seconds (5250.32 seconds total)