Starting phenix.real_space_refine on Fri Jun 13 00:37:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eq2_19894/06_2025/9eq2_19894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eq2_19894/06_2025/9eq2_19894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eq2_19894/06_2025/9eq2_19894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eq2_19894/06_2025/9eq2_19894.map" model { file = "/net/cci-nas-00/data/ceres_data/9eq2_19894/06_2025/9eq2_19894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eq2_19894/06_2025/9eq2_19894.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 92 5.16 5 C 9207 2.51 5 N 2534 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14615 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2292 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 13, 'TRANS': 287} Chain breaks: 2 Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2206 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 2 Chain: "C" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2286 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2292 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 13, 'TRANS': 287} Chain breaks: 2 Chain: "F" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2206 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 2 Chain: "E" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2206 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 2 Chain: "G" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1046 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.02, per 1000 atoms: 0.62 Number of scatterers: 14615 At special positions: 0 Unit cell: (101.31, 129.861, 143.676, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 6 15.00 O 2776 8.00 N 2534 7.00 C 9207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.9 seconds 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3510 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 21 sheets defined 60.2% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 45 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.777A pdb=" N GLY A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.745A pdb=" N SER A 106 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 278 through 293 removed outlier: 3.855A pdb=" N ILE A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 369 through 384 Processing helix chain 'A' and resid 389 through 403 removed outlier: 3.658A pdb=" N LEU A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 411 through 422 Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 441 through 451 Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.454A pdb=" N LEU D 107 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 241 through 248 Processing helix chain 'D' and resid 267 through 283 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 302 through 315 removed outlier: 3.809A pdb=" N ASN D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 360 through 375 Processing helix chain 'D' and resid 380 through 394 Processing helix chain 'D' and resid 395 through 413 removed outlier: 3.791A pdb=" N ALA D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 404 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 429 Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.522A pdb=" N GLN C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.819A pdb=" N GLY C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.922A pdb=" N TYR C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 101 through 105' Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.561A pdb=" N ALA C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 removed outlier: 3.606A pdb=" N ASP C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 292 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 369 through 384 Processing helix chain 'C' and resid 389 through 403 removed outlier: 3.979A pdb=" N LEU C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 428 through 439 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'B' and resid 18 through 22 removed outlier: 3.526A pdb=" N HIS B 21 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 3.563A pdb=" N GLN B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.609A pdb=" N ALA B 65 " --> pdb=" O LYS B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 78 through 91 removed outlier: 4.167A pdb=" N GLY B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 110 through 122 Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 278 through 292 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 353 through 358 removed outlier: 3.705A pdb=" N ASP B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 Processing helix chain 'B' and resid 389 through 403 Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 411 through 421 Processing helix chain 'B' and resid 428 through 438 removed outlier: 3.568A pdb=" N ILE B 432 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'F' and resid 46 through 61 Processing helix chain 'F' and resid 78 through 91 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 241 through 249 Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.951A pdb=" N GLU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 removed outlier: 3.675A pdb=" N MET F 300 " --> pdb=" O GLU F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.627A pdb=" N GLU F 314 " --> pdb=" O ASN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 349 Processing helix chain 'F' and resid 360 through 375 Processing helix chain 'F' and resid 380 through 394 Processing helix chain 'F' and resid 395 through 413 removed outlier: 3.685A pdb=" N THR F 404 " --> pdb=" O ILE F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 430 removed outlier: 3.542A pdb=" N ILE F 423 " --> pdb=" O GLU F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 448 removed outlier: 3.579A pdb=" N TYR F 443 " --> pdb=" O TYR F 439 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN F 446 " --> pdb=" O GLU F 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 61 Processing helix chain 'E' and resid 78 through 91 Processing helix chain 'E' and resid 110 through 122 Processing helix chain 'E' and resid 241 through 249 Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.777A pdb=" N GLU E 314 " --> pdb=" O ASN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 349 Processing helix chain 'E' and resid 360 through 376 Processing helix chain 'E' and resid 380 through 394 Processing helix chain 'E' and resid 395 through 413 removed outlier: 3.668A pdb=" N THR E 404 " --> pdb=" O ILE E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 429 Processing helix chain 'E' and resid 432 through 447 removed outlier: 3.500A pdb=" N TYR E 443 " --> pdb=" O TYR E 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 366 Processing helix chain 'G' and resid 370 through 375 Processing helix chain 'G' and resid 376 through 380 removed outlier: 3.884A pdb=" N THR G 380 " --> pdb=" O LEU G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 383 No H-bonds generated for 'chain 'G' and resid 381 through 383' Processing helix chain 'G' and resid 384 through 389 Processing helix chain 'G' and resid 394 through 408 removed outlier: 3.633A pdb=" N PHE G 408 " --> pdb=" O CYS G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 425 removed outlier: 3.507A pdb=" N GLU G 421 " --> pdb=" O VAL G 417 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 425 " --> pdb=" O GLU G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 435 Processing helix chain 'G' and resid 437 through 451 Processing helix chain 'G' and resid 458 through 474 removed outlier: 3.897A pdb=" N VAL G 464 " --> pdb=" O GLU G 460 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG G 471 " --> pdb=" O LYS G 467 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU G 474 " --> pdb=" O SER G 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 100 removed outlier: 6.281A pdb=" N CYS A 97 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP A 305 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N MET A 99 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A 69 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 334 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 71 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE A 362 " --> pdb=" O LEU D 431 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'D' and resid 96 through 100 removed outlier: 6.550A pdb=" N ALA D 97 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASP D 296 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 99 " --> pdb=" O ASP D 296 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE D 69 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR D 325 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE D 71 " --> pdb=" O THR D 325 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA D 68 " --> pdb=" O LEU D 352 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE D 354 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU D 70 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N THR D 356 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA D 72 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE D 353 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 440 " --> pdb=" O ILE D 353 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 239 through 240 Processing sheet with id=AA7, first strand: chain 'D' and resid 330 through 331 Processing sheet with id=AA8, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 100 removed outlier: 6.248A pdb=" N CYS C 97 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP C 305 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET C 99 " --> pdb=" O ASP C 305 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 69 " --> pdb=" O PHE C 332 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR C 334 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 71 " --> pdb=" O THR C 334 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA C 68 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE C 363 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 70 " --> pdb=" O ILE C 363 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 239 through 242 Processing sheet with id=AB2, first strand: chain 'C' and resid 338 through 340 removed outlier: 3.700A pdb=" N CYS C 339 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 348 " --> pdb=" O CYS C 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 38 through 39 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.776A pdb=" N MET B 99 " --> pdb=" O ASP B 305 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 302 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA B 333 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 304 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 68 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE B 363 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 70 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 362 " --> pdb=" O LEU E 431 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB6, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AB7, first strand: chain 'F' and resid 96 through 98 removed outlier: 5.882A pdb=" N ALA F 97 " --> pdb=" O PHE F 294 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE F 69 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA F 68 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE F 354 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU F 70 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 239 through 240 Processing sheet with id=AB9, first strand: chain 'F' and resid 329 through 331 Processing sheet with id=AC1, first strand: chain 'E' and resid 96 through 99 removed outlier: 5.882A pdb=" N LEU E 293 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA E 324 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE E 295 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 69 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA E 68 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE E 354 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU E 70 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 239 through 240 Processing sheet with id=AC3, first strand: chain 'E' and resid 329 through 331 804 hydrogen bonds defined for protein. 2322 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: 4.44 Time building geometry restraints manager: 3.94 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: 4856 1.34 - 1.46: 2507 1.46 - 1.58: 7260 1.58 - 1.70: 15 1.70 - 1.82: 153 Bond restraints: 14791 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.377 0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C5 ADP A 501 " pdb=" C6 ADP A 501 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" N LYS A 79 " pdb=" CA LYS A 79 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.17e-02 7.31e+03 1.20e+01 ... (remaining 14786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 19167 2.39 - 4.78: 641 4.78 - 7.16: 129 7.16 - 9.55: 25 9.55 - 11.94: 2 Bond angle restraints: 19964 Sorted by residual: angle pdb=" CA THR A 77 " pdb=" CB THR A 77 " pdb=" OG1 THR A 77 " ideal model delta sigma weight residual 109.60 101.44 8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" CA PRO B 370 " pdb=" N PRO B 370 " pdb=" CD PRO B 370 " ideal model delta sigma weight residual 112.00 104.97 7.03 1.40e+00 5.10e-01 2.52e+01 angle pdb=" N VAL C 409 " pdb=" CA VAL C 409 " pdb=" C VAL C 409 " ideal model delta sigma weight residual 113.22 107.30 5.92 1.23e+00 6.61e-01 2.32e+01 angle pdb=" CA GLU E 279 " pdb=" CB GLU E 279 " pdb=" CG GLU E 279 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA THR A 80 " pdb=" CB THR A 80 " pdb=" OG1 THR A 80 " ideal model delta sigma weight residual 109.60 102.56 7.04 1.50e+00 4.44e-01 2.21e+01 ... (remaining 19959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.04: 8807 33.04 - 66.09: 323 66.09 - 99.13: 36 99.13 - 132.17: 2 132.17 - 165.22: 4 Dihedral angle restraints: 9172 sinusoidal: 3768 harmonic: 5404 Sorted by residual: dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 105.22 -165.22 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.87 -146.87 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O2A ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PA ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 156.12 143.88 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 9169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2047 0.072 - 0.143: 306 0.143 - 0.215: 33 0.215 - 0.286: 0 0.286 - 0.358: 2 Chirality restraints: 2388 Sorted by residual: chirality pdb=" CA LEU G 377 " pdb=" N LEU G 377 " pdb=" C LEU G 377 " pdb=" CB LEU G 377 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB VAL C 286 " pdb=" CA VAL C 286 " pdb=" CG1 VAL C 286 " pdb=" CG2 VAL C 286 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB VAL C 43 " pdb=" CA VAL C 43 " pdb=" CG1 VAL C 43 " pdb=" CG2 VAL C 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 2385 not shown) Planarity restraints: 2535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 369 " 0.075 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO B 370 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 428 " 0.273 9.50e-02 1.11e+02 1.23e-01 9.55e+00 pdb=" NE ARG G 428 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG G 428 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 428 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 428 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 289 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO D 290 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 290 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 290 " -0.039 5.00e-02 4.00e+02 ... (remaining 2532 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3649 2.81 - 3.33: 14581 3.33 - 3.86: 23228 3.86 - 4.38: 27636 4.38 - 4.90: 46855 Nonbonded interactions: 115949 Sorted by model distance: nonbonded pdb=" O ASP D 393 " pdb=" NH1 ARG G 428 " model vdw 2.291 3.120 nonbonded pdb=" O SER C 102 " pdb=" OG SER E 307 " model vdw 2.295 3.040 nonbonded pdb=" NZ LYS A 111 " pdb=" OE1 GLU A 313 " model vdw 2.305 3.120 nonbonded pdb=" O ILE D 390 " pdb=" OG1 THR D 394 " model vdw 2.306 3.040 nonbonded pdb=" O THR D 112 " pdb=" OG1 THR D 116 " model vdw 2.342 3.040 ... (remaining 115944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 405 or (resid 406 and (name N or name CA or nam \ e C or name O or name CB )) or resid 407 through 452 or resid 501)) selection = (chain 'B' and (resid 18 through 405 or (resid 406 and (name N or name CA or nam \ e C or name O or name CB )) or resid 407 through 452 or resid 501)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.210 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 14791 Z= 0.309 Angle : 1.031 11.941 19964 Z= 0.539 Chirality : 0.051 0.358 2388 Planarity : 0.007 0.123 2535 Dihedral : 17.345 165.217 5662 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.25 % Allowed : 15.35 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1838 helix: 0.08 (0.15), residues: 1073 sheet: -1.68 (0.30), residues: 236 loop : 0.51 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 280 HIS 0.009 0.001 HIS C 21 PHE 0.024 0.002 PHE B 119 TYR 0.041 0.002 TYR D 443 ARG 0.011 0.001 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.13570 ( 804) hydrogen bonds : angle 5.50831 ( 2322) covalent geometry : bond 0.00694 (14791) covalent geometry : angle 1.03101 (19964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 MET cc_start: 0.7276 (ptm) cc_final: 0.7054 (ptt) outliers start: 4 outliers final: 0 residues processed: 168 average time/residue: 0.2875 time to fit residues: 70.2635 Evaluate side-chains 101 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 89 optimal weight: 0.0170 chunk 109 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 244 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 242 HIS ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.046878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.035833 restraints weight = 90603.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.037062 restraints weight = 50461.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.037857 restraints weight = 34986.971| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14791 Z= 0.130 Angle : 0.595 8.311 19964 Z= 0.294 Chirality : 0.041 0.139 2388 Planarity : 0.005 0.091 2535 Dihedral : 8.935 175.628 2039 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.81 % Allowed : 16.09 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1838 helix: 1.04 (0.15), residues: 1105 sheet: -1.30 (0.32), residues: 221 loop : 0.67 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 280 HIS 0.004 0.001 HIS C 21 PHE 0.020 0.001 PHE C 315 TYR 0.022 0.001 TYR G 357 ARG 0.005 0.000 ARG G 471 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 804) hydrogen bonds : angle 4.09939 ( 2322) covalent geometry : bond 0.00290 (14791) covalent geometry : angle 0.59539 (19964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8808 (mmm) cc_final: 0.8504 (tpt) REVERT: A 309 MET cc_start: 0.9065 (mmm) cc_final: 0.8840 (tpp) REVERT: C 64 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8094 (tpp) REVERT: C 84 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9137 (tp) REVERT: C 116 MET cc_start: 0.9020 (tpt) cc_final: 0.8742 (tpt) REVERT: C 118 ASN cc_start: 0.9144 (m-40) cc_final: 0.8499 (t0) REVERT: B 64 MET cc_start: 0.8604 (tpt) cc_final: 0.8295 (tpt) REVERT: B 283 ASN cc_start: 0.9250 (m-40) cc_final: 0.8835 (m-40) REVERT: F 84 MET cc_start: 0.8932 (mtm) cc_final: 0.8522 (mpp) REVERT: F 317 MET cc_start: 0.8030 (mtt) cc_final: 0.7799 (ttm) REVERT: F 379 MET cc_start: 0.7419 (ppp) cc_final: 0.7132 (ppp) REVERT: E 410 CYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8714 (t) REVERT: G 411 GLU cc_start: 0.9711 (mp0) cc_final: 0.9267 (pp20) REVERT: G 458 PRO cc_start: 0.8991 (Cg_exo) cc_final: 0.8783 (Cg_endo) REVERT: G 461 TYR cc_start: 0.9015 (m-10) cc_final: 0.8779 (m-10) outliers start: 29 outliers final: 8 residues processed: 136 average time/residue: 0.2415 time to fit residues: 52.4811 Evaluate side-chains 111 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 405 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 41 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 308 HIS ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 ASN F 341 HIS G 361 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.044104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033106 restraints weight = 93096.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034247 restraints weight = 52288.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.034983 restraints weight = 36926.163| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14791 Z= 0.255 Angle : 0.658 9.731 19964 Z= 0.323 Chirality : 0.042 0.174 2388 Planarity : 0.004 0.081 2535 Dihedral : 8.564 174.609 2039 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.18 % Allowed : 16.91 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1838 helix: 1.40 (0.16), residues: 1105 sheet: -0.99 (0.33), residues: 212 loop : 0.73 (0.29), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 280 HIS 0.005 0.001 HIS A 23 PHE 0.014 0.002 PHE F 308 TYR 0.020 0.002 TYR D 443 ARG 0.005 0.001 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 804) hydrogen bonds : angle 4.15786 ( 2322) covalent geometry : bond 0.00549 (14791) covalent geometry : angle 0.65776 (19964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 388 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9092 (p) REVERT: C 116 MET cc_start: 0.9035 (tpt) cc_final: 0.8692 (tpt) REVERT: F 84 MET cc_start: 0.8941 (mtm) cc_final: 0.8572 (mpp) REVERT: F 379 MET cc_start: 0.7816 (ppp) cc_final: 0.7392 (ppp) REVERT: E 84 MET cc_start: 0.8725 (mpp) cc_final: 0.8481 (mpp) REVERT: E 410 CYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8826 (t) REVERT: G 404 CYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7698 (t) REVERT: G 440 GLU cc_start: 0.9768 (mp0) cc_final: 0.9463 (pm20) REVERT: G 461 TYR cc_start: 0.9159 (m-10) cc_final: 0.8895 (m-10) outliers start: 35 outliers final: 14 residues processed: 130 average time/residue: 0.2723 time to fit residues: 57.0057 Evaluate side-chains 108 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 388 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 119 PHE Chi-restraints excluded: chain F residue 280 TRP Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Chi-restraints excluded: chain G residue 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 114 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 129 optimal weight: 0.0000 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN F 74 GLN E 74 GLN G 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.045390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.033763 restraints weight = 93997.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.034999 restraints weight = 51139.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.035802 restraints weight = 35441.887| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14791 Z= 0.119 Angle : 0.559 8.804 19964 Z= 0.269 Chirality : 0.040 0.140 2388 Planarity : 0.004 0.065 2535 Dihedral : 8.169 167.840 2039 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.93 % Allowed : 17.47 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.20), residues: 1838 helix: 1.60 (0.16), residues: 1103 sheet: -0.84 (0.32), residues: 217 loop : 0.87 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 280 HIS 0.003 0.001 HIS C 21 PHE 0.015 0.001 PHE E 119 TYR 0.018 0.001 TYR D 443 ARG 0.003 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 804) hydrogen bonds : angle 3.77828 ( 2322) covalent geometry : bond 0.00267 (14791) covalent geometry : angle 0.55892 (19964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 109 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7734 (pmm) REVERT: C 116 MET cc_start: 0.8978 (tpt) cc_final: 0.8687 (tpt) REVERT: C 118 ASN cc_start: 0.9289 (m-40) cc_final: 0.9001 (t0) REVERT: F 84 MET cc_start: 0.8977 (mtm) cc_final: 0.8505 (mpp) REVERT: F 300 MET cc_start: 0.8917 (mmm) cc_final: 0.8557 (mmm) REVERT: F 408 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9137 (tt) REVERT: E 84 MET cc_start: 0.8728 (mpp) cc_final: 0.8493 (mpp) REVERT: E 119 PHE cc_start: 0.9162 (t80) cc_final: 0.8912 (t80) REVERT: E 410 CYS cc_start: 0.8942 (OUTLIER) cc_final: 0.7824 (t) REVERT: G 404 CYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7596 (t) REVERT: G 440 GLU cc_start: 0.9789 (mp0) cc_final: 0.9454 (pm20) REVERT: G 461 TYR cc_start: 0.9174 (m-10) cc_final: 0.8899 (m-10) outliers start: 31 outliers final: 15 residues processed: 130 average time/residue: 0.2880 time to fit residues: 60.4293 Evaluate side-chains 116 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 119 PHE Chi-restraints excluded: chain F residue 280 TRP Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Chi-restraints excluded: chain G residue 419 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 33 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN C 61 GLN ** E 242 HIS ** 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 = 0.3136 r_free = 0.3136 target = 0.043194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.031658 restraints weight = 97447.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032840 restraints weight = 53440.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.033594 restraints weight = 37185.543| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14791 Z= 0.299 Angle : 0.697 9.364 19964 Z= 0.340 Chirality : 0.043 0.221 2388 Planarity : 0.004 0.069 2535 Dihedral : 7.921 149.305 2039 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.06 % Allowed : 16.97 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1838 helix: 1.48 (0.16), residues: 1101 sheet: -0.72 (0.33), residues: 212 loop : 0.80 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 280 HIS 0.005 0.001 HIS D 242 PHE 0.016 0.002 PHE E 119 TYR 0.026 0.002 TYR G 357 ARG 0.007 0.001 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 804) hydrogen bonds : angle 4.22666 ( 2322) covalent geometry : bond 0.00640 (14791) covalent geometry : angle 0.69661 (19964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 96 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 109 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8272 (ppp) REVERT: D 388 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9149 (p) REVERT: C 426 ASN cc_start: 0.9000 (m-40) cc_final: 0.8774 (p0) REVERT: F 84 MET cc_start: 0.9006 (mtm) cc_final: 0.8581 (mpp) REVERT: F 287 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: F 437 MET cc_start: 0.8922 (tpt) cc_final: 0.8489 (tpp) REVERT: E 84 MET cc_start: 0.8800 (mpp) cc_final: 0.8592 (mpp) REVERT: E 410 CYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8638 (t) REVERT: G 404 CYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7379 (t) outliers start: 49 outliers final: 30 residues processed: 137 average time/residue: 0.2567 time to fit residues: 53.7876 Evaluate side-chains 125 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 388 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 105 PHE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 280 TRP Chi-restraints excluded: chain F residue 287 GLU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Chi-restraints excluded: chain G residue 459 MET Chi-restraints excluded: chain G residue 464 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 170 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 174 optimal weight: 0.0470 chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 185 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.044661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.033214 restraints weight = 95123.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.034420 restraints weight = 51876.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.035206 restraints weight = 36094.959| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14791 Z= 0.108 Angle : 0.570 8.763 19964 Z= 0.274 Chirality : 0.040 0.139 2388 Planarity : 0.004 0.053 2535 Dihedral : 7.576 140.170 2039 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.62 % Allowed : 18.90 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.20), residues: 1838 helix: 1.60 (0.16), residues: 1104 sheet: -0.63 (0.33), residues: 217 loop : 0.88 (0.30), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 280 HIS 0.002 0.000 HIS C 21 PHE 0.012 0.001 PHE G 408 TYR 0.018 0.001 TYR D 443 ARG 0.008 0.000 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.02903 ( 804) hydrogen bonds : angle 3.76301 ( 2322) covalent geometry : bond 0.00243 (14791) covalent geometry : angle 0.56989 (19964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 1.913 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: A 79 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8112 (mttp) REVERT: D 109 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8259 (ppp) REVERT: C 118 ASN cc_start: 0.9313 (m-40) cc_final: 0.9026 (t0) REVERT: F 57 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9167 (tp40) REVERT: F 84 MET cc_start: 0.8972 (mtm) cc_final: 0.8471 (mpp) REVERT: F 379 MET cc_start: 0.7405 (ppp) cc_final: 0.7128 (ppp) REVERT: E 119 PHE cc_start: 0.9189 (t80) cc_final: 0.8881 (t80) REVERT: E 379 MET cc_start: 0.8860 (mmm) cc_final: 0.8601 (mmm) REVERT: E 410 CYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8721 (t) REVERT: G 404 CYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7234 (t) REVERT: G 413 MET cc_start: 0.9037 (mmm) cc_final: 0.8818 (mmm) REVERT: G 440 GLU cc_start: 0.9746 (mp0) cc_final: 0.9409 (pm20) REVERT: G 452 PHE cc_start: 0.9219 (m-80) cc_final: 0.8905 (m-80) REVERT: G 461 TYR cc_start: 0.9170 (m-10) cc_final: 0.8967 (m-10) outliers start: 26 outliers final: 18 residues processed: 123 average time/residue: 0.2788 time to fit residues: 54.4047 Evaluate side-chains 121 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain F residue 57 GLN Chi-restraints excluded: chain F residue 119 PHE Chi-restraints excluded: chain F residue 280 TRP Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Chi-restraints excluded: chain G residue 464 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 42 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.044034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.032699 restraints weight = 94406.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.033885 restraints weight = 50782.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034672 restraints weight = 35013.919| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14791 Z= 0.166 Angle : 0.589 8.349 19964 Z= 0.284 Chirality : 0.040 0.142 2388 Planarity : 0.004 0.053 2535 Dihedral : 7.365 133.598 2039 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.56 % Allowed : 18.53 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.21), residues: 1838 helix: 1.64 (0.16), residues: 1104 sheet: -0.53 (0.33), residues: 215 loop : 0.97 (0.30), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 280 HIS 0.003 0.001 HIS E 299 PHE 0.014 0.001 PHE G 408 TYR 0.023 0.001 TYR G 357 ARG 0.007 0.000 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 804) hydrogen bonds : angle 3.81565 ( 2322) covalent geometry : bond 0.00364 (14791) covalent geometry : angle 0.58901 (19964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 99 ILE cc_start: 0.9627 (OUTLIER) cc_final: 0.9402 (mp) REVERT: D 109 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8225 (ppp) REVERT: C 64 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8261 (tpp) REVERT: B 64 MET cc_start: 0.8242 (tpt) cc_final: 0.7985 (tpt) REVERT: F 84 MET cc_start: 0.8987 (mtm) cc_final: 0.8496 (mpp) REVERT: F 379 MET cc_start: 0.7494 (ppp) cc_final: 0.7207 (ppp) REVERT: F 437 MET cc_start: 0.8956 (tpt) cc_final: 0.8522 (tpp) REVERT: E 84 MET cc_start: 0.8826 (mpp) cc_final: 0.8541 (mpp) REVERT: E 119 PHE cc_start: 0.9215 (t80) cc_final: 0.8906 (t80) REVERT: E 379 MET cc_start: 0.8815 (mmm) cc_final: 0.8546 (mmm) REVERT: E 410 CYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8744 (t) REVERT: G 360 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9039 (tp30) REVERT: G 404 CYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7389 (t) REVERT: G 413 MET cc_start: 0.9014 (mmm) cc_final: 0.8796 (mmm) REVERT: G 440 GLU cc_start: 0.9746 (mp0) cc_final: 0.9408 (pm20) REVERT: G 461 TYR cc_start: 0.9148 (m-10) cc_final: 0.8913 (m-10) outliers start: 41 outliers final: 27 residues processed: 132 average time/residue: 0.2540 time to fit residues: 53.9028 Evaluate side-chains 125 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 119 PHE Chi-restraints excluded: chain F residue 280 TRP Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Chi-restraints excluded: chain G residue 464 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 179 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.044730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.033301 restraints weight = 94812.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.034506 restraints weight = 51905.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.035300 restraints weight = 36157.880| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14791 Z= 0.110 Angle : 0.571 8.872 19964 Z= 0.273 Chirality : 0.040 0.152 2388 Planarity : 0.004 0.053 2535 Dihedral : 7.174 129.910 2039 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.12 % Allowed : 18.59 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.21), residues: 1838 helix: 1.63 (0.16), residues: 1106 sheet: -0.50 (0.33), residues: 217 loop : 1.04 (0.30), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 280 HIS 0.003 0.001 HIS E 299 PHE 0.013 0.001 PHE G 408 TYR 0.017 0.001 TYR G 357 ARG 0.007 0.000 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.02768 ( 804) hydrogen bonds : angle 3.65465 ( 2322) covalent geometry : bond 0.00251 (14791) covalent geometry : angle 0.57125 (19964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8036 (mttp) REVERT: A 312 MET cc_start: 0.9280 (mmm) cc_final: 0.9013 (mmm) REVERT: D 99 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9343 (mp) REVERT: B 64 MET cc_start: 0.8161 (tpt) cc_final: 0.7960 (tpt) REVERT: F 84 MET cc_start: 0.8940 (mtm) cc_final: 0.8433 (mpp) REVERT: F 379 MET cc_start: 0.7565 (ppp) cc_final: 0.7282 (ppp) REVERT: F 437 MET cc_start: 0.8965 (tpt) cc_final: 0.8668 (tpt) REVERT: E 84 MET cc_start: 0.8798 (mpp) cc_final: 0.8481 (mpp) REVERT: E 119 PHE cc_start: 0.9204 (t80) cc_final: 0.8903 (t80) REVERT: E 379 MET cc_start: 0.8806 (mmm) cc_final: 0.8533 (mmm) REVERT: E 410 CYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8751 (t) REVERT: G 360 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9054 (tp30) REVERT: G 404 CYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7360 (t) REVERT: G 440 GLU cc_start: 0.9737 (mp0) cc_final: 0.9400 (pm20) REVERT: G 452 PHE cc_start: 0.9226 (m-80) cc_final: 0.8902 (m-80) REVERT: G 461 TYR cc_start: 0.9221 (m-10) cc_final: 0.8979 (m-10) outliers start: 34 outliers final: 23 residues processed: 127 average time/residue: 0.2341 time to fit residues: 46.8068 Evaluate side-chains 121 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain F residue 119 PHE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 280 TRP Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 20 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.044584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.033122 restraints weight = 94773.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.034308 restraints weight = 51891.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035088 restraints weight = 36284.778| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14791 Z= 0.127 Angle : 0.586 13.364 19964 Z= 0.280 Chirality : 0.040 0.163 2388 Planarity : 0.004 0.054 2535 Dihedral : 7.022 125.356 2039 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.06 % Allowed : 18.71 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1838 helix: 1.67 (0.16), residues: 1104 sheet: -0.50 (0.33), residues: 217 loop : 1.05 (0.30), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 280 HIS 0.003 0.001 HIS E 299 PHE 0.013 0.001 PHE G 408 TYR 0.019 0.001 TYR G 357 ARG 0.006 0.000 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.02795 ( 804) hydrogen bonds : angle 3.66379 ( 2322) covalent geometry : bond 0.00286 (14791) covalent geometry : angle 0.58628 (19964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8033 (mttp) REVERT: A 312 MET cc_start: 0.9262 (mmm) cc_final: 0.9001 (mmm) REVERT: D 99 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9367 (mp) REVERT: C 64 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8236 (tpp) REVERT: C 118 ASN cc_start: 0.9295 (m-40) cc_final: 0.9003 (t0) REVERT: B 64 MET cc_start: 0.8128 (tpt) cc_final: 0.7906 (tpt) REVERT: F 84 MET cc_start: 0.8917 (mtm) cc_final: 0.8442 (mpp) REVERT: F 379 MET cc_start: 0.7613 (ppp) cc_final: 0.7339 (ppp) REVERT: F 437 MET cc_start: 0.8950 (tpt) cc_final: 0.8652 (tpt) REVERT: E 84 MET cc_start: 0.8788 (mpp) cc_final: 0.8463 (mpp) REVERT: E 119 PHE cc_start: 0.9192 (t80) cc_final: 0.8898 (t80) REVERT: E 379 MET cc_start: 0.8768 (mmm) cc_final: 0.8509 (mmm) REVERT: E 410 CYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8774 (t) REVERT: G 360 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9059 (tp30) REVERT: G 404 CYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7409 (t) REVERT: G 440 GLU cc_start: 0.9729 (mp0) cc_final: 0.9390 (pm20) REVERT: G 452 PHE cc_start: 0.9206 (m-80) cc_final: 0.8884 (m-80) outliers start: 33 outliers final: 25 residues processed: 125 average time/residue: 0.2512 time to fit residues: 50.2727 Evaluate side-chains 125 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain F residue 119 PHE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 280 TRP Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 115 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.043126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.031731 restraints weight = 96543.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.032874 restraints weight = 53353.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.033623 restraints weight = 37339.403| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14791 Z= 0.256 Angle : 0.693 13.181 19964 Z= 0.333 Chirality : 0.042 0.158 2388 Planarity : 0.004 0.054 2535 Dihedral : 7.049 128.127 2039 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.00 % Allowed : 18.59 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1838 helix: 1.61 (0.16), residues: 1095 sheet: -0.57 (0.33), residues: 218 loop : 1.00 (0.30), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 280 HIS 0.006 0.001 HIS E 299 PHE 0.013 0.002 PHE G 408 TYR 0.035 0.002 TYR G 357 ARG 0.008 0.001 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 804) hydrogen bonds : angle 4.01823 ( 2322) covalent geometry : bond 0.00553 (14791) covalent geometry : angle 0.69326 (19964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3676 Ramachandran restraints generated. 1838 Oldfield, 0 Emsley, 1838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8936 (tpt) cc_final: 0.8712 (tpp) REVERT: C 64 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8198 (tpp) REVERT: B 64 MET cc_start: 0.8350 (tpt) cc_final: 0.8086 (tpt) REVERT: F 84 MET cc_start: 0.8972 (mtm) cc_final: 0.8511 (mpp) REVERT: F 379 MET cc_start: 0.7660 (ppp) cc_final: 0.7371 (ppp) REVERT: E 84 MET cc_start: 0.8853 (mpp) cc_final: 0.8595 (mpp) REVERT: E 119 PHE cc_start: 0.9180 (t80) cc_final: 0.8645 (t80) REVERT: E 315 ASN cc_start: 0.9394 (m-40) cc_final: 0.8763 (p0) REVERT: E 379 MET cc_start: 0.8808 (mmm) cc_final: 0.8550 (mmm) REVERT: E 410 CYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8808 (t) REVERT: G 360 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9096 (tp30) REVERT: G 404 CYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7286 (t) REVERT: G 440 GLU cc_start: 0.9719 (mp0) cc_final: 0.9396 (pm20) outliers start: 32 outliers final: 24 residues processed: 123 average time/residue: 0.2363 time to fit residues: 45.7370 Evaluate side-chains 119 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 450 HIS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 280 TRP Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 410 CYS Chi-restraints excluded: chain E residue 426 VAL Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 149 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.044860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.033468 restraints weight = 95218.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.034674 restraints weight = 51903.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.035473 restraints weight = 36052.776| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14791 Z= 0.103 Angle : 0.593 10.863 19964 Z= 0.283 Chirality : 0.041 0.164 2388 Planarity : 0.004 0.054 2535 Dihedral : 6.760 127.176 2039 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.56 % Allowed : 19.46 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1838 helix: 1.66 (0.16), residues: 1096 sheet: -0.48 (0.33), residues: 218 loop : 1.01 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 280 HIS 0.006 0.001 HIS E 299 PHE 0.016 0.001 PHE D 119 TYR 0.036 0.001 TYR G 357 ARG 0.010 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.02746 ( 804) hydrogen bonds : angle 3.63161 ( 2322) covalent geometry : bond 0.00233 (14791) covalent geometry : angle 0.59341 (19964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5530.18 seconds wall clock time: 100 minutes 36.45 seconds (6036.45 seconds total)