Starting phenix.real_space_refine on Thu Sep 18 05:53:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eq2_19894/09_2025/9eq2_19894.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eq2_19894/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9eq2_19894/09_2025/9eq2_19894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eq2_19894/09_2025/9eq2_19894.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eq2_19894/09_2025/9eq2_19894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eq2_19894/09_2025/9eq2_19894.map" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.42, per 1000 atoms: 0.23 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: 1.01 Conformation dependent library (CDL) restraints added in 525.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.48 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: 2.12 Time building geometry restraints manager: 1.31 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 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 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: 2.110 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.870 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.530 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG D 270 TYR 0.041 0.002 TYR D 443 PHE 0.024 0.002 PHE B 119 TRP 0.033 0.003 TRP E 280 HIS 0.009 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00694 (14791) covalent geometry : angle 1.03101 (19964) hydrogen bonds : bond 0.13570 ( 804) hydrogen bonds : angle 5.50831 ( 2322) *********************** 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 : 0.524 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: 0.7053 (ptt) outliers start: 4 outliers final: 0 residues processed: 168 average time/residue: 0.1309 time to fit residues: 32.1913 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 : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 242 HIS ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.047105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.036340 restraints weight = 89499.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.037530 restraints weight = 48998.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.038352 restraints weight = 33882.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038813 restraints weight = 26514.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039189 restraints weight = 22941.103| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14791 Z= 0.121 Angle : 0.592 8.233 19964 Z= 0.292 Chirality : 0.041 0.138 2388 Planarity : 0.005 0.090 2535 Dihedral : 8.946 175.763 2039 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.81 % Allowed : 15.97 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.20), residues: 1838 helix: 1.00 (0.15), residues: 1105 sheet: -1.29 (0.32), residues: 221 loop : 0.65 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 471 TYR 0.022 0.001 TYR D 443 PHE 0.019 0.001 PHE C 315 TRP 0.018 0.002 TRP F 280 HIS 0.004 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00270 (14791) covalent geometry : angle 0.59222 (19964) hydrogen bonds : bond 0.03429 ( 804) hydrogen bonds : angle 4.10595 ( 2322) *********************** 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 139 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8826 (mmm) cc_final: 0.8528 (tpt) REVERT: C 64 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8221 (tpt) REVERT: C 84 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9124 (tp) REVERT: C 116 MET cc_start: 0.9011 (tpt) cc_final: 0.8735 (tpt) REVERT: C 118 ASN cc_start: 0.9175 (m-40) cc_final: 0.8526 (t0) REVERT: F 84 MET cc_start: 0.8901 (mtm) cc_final: 0.8504 (mpp) REVERT: F 379 MET cc_start: 0.7482 (ppp) cc_final: 0.7001 (ppp) REVERT: G 411 GLU cc_start: 0.9683 (mp0) cc_final: 0.9187 (pp20) REVERT: G 461 TYR cc_start: 0.8902 (m-10) cc_final: 0.8687 (m-10) outliers start: 29 outliers final: 7 residues processed: 135 average time/residue: 0.1002 time to fit residues: 21.6861 Evaluate side-chains 109 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 278 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain F residue 330 THR 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 48 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 ASN F 341 HIS E 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.044368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.032707 restraints weight = 96288.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.033903 restraints weight = 52951.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.034698 restraints weight = 36904.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.035184 restraints weight = 29334.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.035543 restraints weight = 25477.529| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14791 Z= 0.255 Angle : 0.665 9.896 19964 Z= 0.328 Chirality : 0.042 0.160 2388 Planarity : 0.005 0.083 2535 Dihedral : 8.550 173.523 2039 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.25 % Allowed : 17.53 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.20), residues: 1838 helix: 1.38 (0.16), residues: 1104 sheet: -0.87 (0.33), residues: 208 loop : 0.72 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 311 TYR 0.021 0.002 TYR G 357 PHE 0.015 0.002 PHE F 308 TRP 0.033 0.003 TRP F 280 HIS 0.006 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00551 (14791) covalent geometry : angle 0.66516 (19964) hydrogen bonds : bond 0.03625 ( 804) hydrogen bonds : angle 4.17093 ( 2322) *********************** 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 137 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 388 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9076 (p) REVERT: D 437 MET cc_start: 0.9021 (ttp) cc_final: 0.8796 (ttp) REVERT: C 64 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8411 (tmm) REVERT: C 116 MET cc_start: 0.9033 (tpt) cc_final: 0.8715 (tpt) REVERT: F 84 MET cc_start: 0.8946 (mtm) cc_final: 0.8578 (mpp) REVERT: F 379 MET cc_start: 0.7867 (ppp) cc_final: 0.7476 (ppp) REVERT: G 404 CYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7781 (t) REVERT: G 440 GLU cc_start: 0.9777 (mp0) cc_final: 0.9485 (pm20) REVERT: G 461 TYR cc_start: 0.9150 (m-10) cc_final: 0.8837 (m-10) outliers start: 36 outliers final: 16 residues processed: 131 average time/residue: 0.0987 time to fit residues: 20.6815 Evaluate side-chains 108 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 388 THR 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 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 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 439 TYR 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 405 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 162 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 27 optimal weight: 0.0040 chunk 173 optimal weight: 0.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN G 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.044969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033321 restraints weight = 94693.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.034557 restraints weight = 51563.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.035328 restraints weight = 35691.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.035854 restraints weight = 28498.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.036187 restraints weight = 24619.771| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3104 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= 0.137 Angle : 0.573 8.845 19964 Z= 0.277 Chirality : 0.041 0.238 2388 Planarity : 0.004 0.066 2535 Dihedral : 8.192 168.048 2039 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.31 % Allowed : 17.28 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.20), residues: 1838 helix: 1.58 (0.16), residues: 1103 sheet: -0.89 (0.32), residues: 221 loop : 0.93 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.018 0.001 TYR D 443 PHE 0.015 0.001 PHE E 119 TRP 0.026 0.002 TRP F 280 HIS 0.003 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00305 (14791) covalent geometry : angle 0.57337 (19964) hydrogen bonds : bond 0.02999 ( 804) hydrogen bonds : angle 3.84642 ( 2322) *********************** 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 139 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 109 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7614 (pmm) REVERT: D 437 MET cc_start: 0.9040 (ttp) cc_final: 0.8783 (ttp) REVERT: C 64 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8269 (tpp) REVERT: C 116 MET cc_start: 0.8981 (tpt) cc_final: 0.8757 (tpt) REVERT: C 118 ASN cc_start: 0.9325 (m-40) cc_final: 0.9064 (t0) REVERT: F 84 MET cc_start: 0.8969 (mtm) cc_final: 0.8506 (mpp) REVERT: F 300 MET cc_start: 0.8900 (mmm) cc_final: 0.8536 (mmm) REVERT: F 379 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7747 (ppp) REVERT: G 404 CYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7650 (t) REVERT: G 440 GLU cc_start: 0.9783 (mp0) cc_final: 0.9473 (pm20) REVERT: G 461 TYR cc_start: 0.9024 (m-10) cc_final: 0.8788 (m-10) outliers start: 37 outliers final: 19 residues processed: 131 average time/residue: 0.1108 time to fit residues: 22.6258 Evaluate side-chains 120 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 64 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 318 LEU Chi-restraints excluded: chain F residue 98 MET 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 379 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 269 VAL 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 419 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 63 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.044880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033320 restraints weight = 94268.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.034522 restraints weight = 52154.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.035311 restraints weight = 36432.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.035788 restraints weight = 28998.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.036153 restraints weight = 25243.611| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14791 Z= 0.134 Angle : 0.565 7.750 19964 Z= 0.272 Chirality : 0.040 0.144 2388 Planarity : 0.004 0.059 2535 Dihedral : 7.828 155.622 2039 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.00 % Allowed : 17.97 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.20), residues: 1838 helix: 1.61 (0.16), residues: 1104 sheet: -0.66 (0.33), residues: 217 loop : 1.02 (0.30), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 413 TYR 0.017 0.001 TYR G 357 PHE 0.010 0.001 PHE F 308 TRP 0.024 0.002 TRP F 280 HIS 0.003 0.000 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00298 (14791) covalent geometry : angle 0.56457 (19964) hydrogen bonds : bond 0.02913 ( 804) hydrogen bonds : angle 3.74827 ( 2322) *********************** 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 134 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 437 MET cc_start: 0.9010 (ttp) cc_final: 0.8711 (ttp) REVERT: C 64 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8254 (tpp) REVERT: C 118 ASN cc_start: 0.9309 (m-40) cc_final: 0.9046 (t0) REVERT: C 426 ASN cc_start: 0.8959 (m-40) cc_final: 0.8758 (p0) REVERT: B 64 MET cc_start: 0.8101 (tpt) cc_final: 0.7836 (tpt) REVERT: F 57 GLN cc_start: 0.9570 (OUTLIER) cc_final: 0.9292 (tp40) REVERT: F 84 MET cc_start: 0.8908 (mtm) cc_final: 0.8454 (mpp) REVERT: F 300 MET cc_start: 0.8997 (mmm) cc_final: 0.8624 (mmm) REVERT: F 379 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7764 (ppp) REVERT: E 84 MET cc_start: 0.8733 (mpp) cc_final: 0.8457 (mpp) REVERT: E 379 MET cc_start: 0.8721 (mmm) cc_final: 0.8500 (mmm) REVERT: G 404 CYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7383 (t) REVERT: G 440 GLU cc_start: 0.9787 (mp0) cc_final: 0.9582 (mp0) outliers start: 32 outliers final: 21 residues processed: 126 average time/residue: 0.1084 time to fit residues: 21.7370 Evaluate side-chains 120 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 279 ARG 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 421 MET 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 99 ILE 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 379 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 77 THR 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 151 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS C 61 GLN ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.045437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033903 restraints weight = 93880.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.035155 restraints weight = 51104.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.035968 restraints weight = 35251.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036486 restraints weight = 27869.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.036804 restraints weight = 24038.520| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14791 Z= 0.101 Angle : 0.538 8.640 19964 Z= 0.260 Chirality : 0.040 0.140 2388 Planarity : 0.004 0.055 2535 Dihedral : 7.460 139.069 2039 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.18 % Allowed : 17.84 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.20), residues: 1838 helix: 1.60 (0.16), residues: 1106 sheet: -0.72 (0.33), residues: 224 loop : 1.05 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 413 TYR 0.015 0.001 TYR D 443 PHE 0.015 0.001 PHE E 119 TRP 0.022 0.001 TRP F 280 HIS 0.003 0.000 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00225 (14791) covalent geometry : angle 0.53823 (19964) hydrogen bonds : bond 0.02724 ( 804) hydrogen bonds : angle 3.62909 ( 2322) *********************** 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 135 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.629 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: D 58 MET cc_start: 0.9052 (mtt) cc_final: 0.8845 (ttm) REVERT: D 437 MET cc_start: 0.9018 (ttp) cc_final: 0.8695 (ttp) REVERT: C 64 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8193 (tpp) REVERT: C 118 ASN cc_start: 0.9291 (m-40) cc_final: 0.9047 (t0) REVERT: C 426 ASN cc_start: 0.9002 (m-40) cc_final: 0.8776 (p0) REVERT: B 64 MET cc_start: 0.8130 (tpt) cc_final: 0.7864 (tpt) REVERT: F 57 GLN cc_start: 0.9565 (OUTLIER) cc_final: 0.9298 (tp40) REVERT: F 84 MET cc_start: 0.8906 (mtm) cc_final: 0.8414 (mpp) REVERT: F 300 MET cc_start: 0.9059 (mmm) cc_final: 0.8679 (mmm) REVERT: F 379 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7756 (ppp) REVERT: E 119 PHE cc_start: 0.9167 (t80) cc_final: 0.8940 (t80) REVERT: G 404 CYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7434 (t) REVERT: G 413 MET cc_start: 0.9002 (mmm) cc_final: 0.8780 (mmm) REVERT: G 440 GLU cc_start: 0.9782 (mp0) cc_final: 0.9549 (mp0) REVERT: G 452 PHE cc_start: 0.9148 (m-80) cc_final: 0.8888 (m-80) outliers start: 35 outliers final: 21 residues processed: 130 average time/residue: 0.1114 time to fit residues: 22.4117 Evaluate side-chains 121 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 279 ARG 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 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 335 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 77 THR 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 129 optimal weight: 0.7980 chunk 155 optimal weight: 0.0970 chunk 128 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 99 optimal weight: 0.0570 chunk 58 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 118 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 = 0.3227 r_free = 0.3227 target = 0.045886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.034453 restraints weight = 94044.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035687 restraints weight = 51481.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036494 restraints weight = 35712.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.037009 restraints weight = 28348.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.037338 restraints weight = 24492.266| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3688 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= 0.095 Angle : 0.556 14.595 19964 Z= 0.263 Chirality : 0.040 0.213 2388 Planarity : 0.004 0.055 2535 Dihedral : 7.207 129.729 2039 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.25 % Allowed : 18.15 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.20), residues: 1838 helix: 1.60 (0.16), residues: 1108 sheet: -0.62 (0.33), residues: 224 loop : 1.05 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 392 TYR 0.014 0.001 TYR D 443 PHE 0.013 0.001 PHE E 119 TRP 0.021 0.001 TRP F 280 HIS 0.003 0.000 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00213 (14791) covalent geometry : angle 0.55610 (19964) hydrogen bonds : bond 0.02643 ( 804) hydrogen bonds : angle 3.57453 ( 2322) *********************** 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 137 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 58 MET cc_start: 0.9040 (mtt) cc_final: 0.8809 (ttm) REVERT: D 437 MET cc_start: 0.9000 (ttp) cc_final: 0.8698 (ttp) REVERT: C 64 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8184 (tpp) REVERT: C 116 MET cc_start: 0.9234 (mmm) cc_final: 0.8433 (mmm) REVERT: C 118 ASN cc_start: 0.9293 (m-40) cc_final: 0.8950 (t0) REVERT: C 426 ASN cc_start: 0.9043 (m-40) cc_final: 0.8797 (p0) REVERT: B 309 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8388 (tpp) REVERT: F 84 MET cc_start: 0.8914 (mtm) cc_final: 0.8418 (mpp) REVERT: F 300 MET cc_start: 0.9050 (mmm) cc_final: 0.8651 (mmm) REVERT: F 379 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7686 (ppp) REVERT: E 119 PHE cc_start: 0.9180 (t80) cc_final: 0.8939 (t80) REVERT: G 404 CYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7382 (t) REVERT: G 440 GLU cc_start: 0.9785 (mp0) cc_final: 0.9545 (mp0) REVERT: G 452 PHE cc_start: 0.9118 (m-80) cc_final: 0.8877 (m-80) outliers start: 36 outliers final: 22 residues processed: 130 average time/residue: 0.1204 time to fit residues: 24.4176 Evaluate side-chains 125 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 318 LEU 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 315 PHE 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 294 VAL Chi-restraints excluded: chain B residue 309 MET 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 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain G residue 381 THR Chi-restraints excluded: chain G residue 404 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 49 optimal weight: 0.0040 chunk 17 optimal weight: 0.0010 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 GLN ** D 242 HIS ** 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 = 0.3195 r_free = 0.3195 target = 0.044944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.033519 restraints weight = 95324.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.034741 restraints weight = 52245.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.035522 restraints weight = 36216.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.036004 restraints weight = 28839.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.036354 restraints weight = 25024.317| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3824 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= 0.139 Angle : 0.581 9.159 19964 Z= 0.276 Chirality : 0.040 0.257 2388 Planarity : 0.004 0.055 2535 Dihedral : 7.062 127.371 2039 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.12 % Allowed : 18.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.21), residues: 1838 helix: 1.67 (0.16), residues: 1104 sheet: -0.60 (0.33), residues: 224 loop : 1.13 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 392 TYR 0.013 0.001 TYR D 443 PHE 0.014 0.001 PHE E 119 TRP 0.019 0.002 TRP F 280 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00311 (14791) covalent geometry : angle 0.58114 (19964) hydrogen bonds : bond 0.02761 ( 804) hydrogen bonds : angle 3.66502 ( 2322) *********************** 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 : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 437 MET cc_start: 0.9002 (ttp) cc_final: 0.8689 (ttp) REVERT: C 64 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8220 (tpp) REVERT: C 116 MET cc_start: 0.9192 (mmm) cc_final: 0.8979 (mmm) REVERT: C 118 ASN cc_start: 0.9285 (m-40) cc_final: 0.8923 (t0) REVERT: C 426 ASN cc_start: 0.9037 (m-40) cc_final: 0.8810 (p0) REVERT: F 84 MET cc_start: 0.8913 (mtm) cc_final: 0.8419 (mpp) REVERT: F 300 MET cc_start: 0.9061 (mmm) cc_final: 0.8637 (mmm) REVERT: F 379 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7624 (ppp) REVERT: E 84 MET cc_start: 0.9140 (mtm) cc_final: 0.8703 (mpp) REVERT: E 98 MET cc_start: 0.8440 (tpt) cc_final: 0.8205 (tpt) REVERT: E 119 PHE cc_start: 0.9197 (t80) cc_final: 0.8959 (t80) REVERT: G 357 TYR cc_start: 0.8049 (t80) cc_final: 0.7812 (t80) REVERT: G 404 CYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7513 (t) REVERT: G 440 GLU cc_start: 0.9786 (mp0) cc_final: 0.9551 (mp0) outliers start: 34 outliers final: 24 residues processed: 127 average time/residue: 0.1211 time to fit residues: 24.0928 Evaluate side-chains 120 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 421 MET Chi-restraints excluded: chain C residue 450 HIS 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 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 266 ARG 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 85 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3190 r_free = 0.3190 target = 0.044717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.033230 restraints weight = 95504.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.034458 restraints weight = 52518.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.035230 restraints weight = 36437.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.035726 restraints weight = 29122.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036062 restraints weight = 25306.475| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14791 Z= 0.149 Angle : 0.609 13.492 19964 Z= 0.287 Chirality : 0.041 0.200 2388 Planarity : 0.004 0.054 2535 Dihedral : 6.947 122.757 2039 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.81 % Allowed : 18.84 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.21), residues: 1838 helix: 1.69 (0.16), residues: 1104 sheet: -0.58 (0.33), residues: 224 loop : 1.13 (0.30), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 392 TYR 0.016 0.001 TYR D 443 PHE 0.014 0.001 PHE E 119 TRP 0.019 0.001 TRP F 280 HIS 0.004 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00332 (14791) covalent geometry : angle 0.60878 (19964) hydrogen bonds : bond 0.02782 ( 804) hydrogen bonds : angle 3.67897 ( 2322) *********************** 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 125 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 437 MET cc_start: 0.9004 (ttp) cc_final: 0.8701 (ttp) REVERT: C 64 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8244 (tpp) REVERT: C 118 ASN cc_start: 0.9248 (m-40) cc_final: 0.8955 (t0) REVERT: F 84 MET cc_start: 0.8875 (mtm) cc_final: 0.8406 (mpp) REVERT: F 300 MET cc_start: 0.9069 (mmm) cc_final: 0.8614 (mmm) REVERT: F 379 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7639 (ppp) REVERT: F 437 MET cc_start: 0.8939 (tpt) cc_final: 0.8691 (tpt) REVERT: E 98 MET cc_start: 0.8418 (tpt) cc_final: 0.8203 (tpt) REVERT: E 119 PHE cc_start: 0.9196 (t80) cc_final: 0.8920 (t80) REVERT: G 404 CYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7504 (t) REVERT: G 440 GLU cc_start: 0.9804 (mp0) cc_final: 0.9511 (pm20) outliers start: 29 outliers final: 21 residues processed: 119 average time/residue: 0.1164 time to fit residues: 21.9685 Evaluate side-chains 116 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 408 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 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 330 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain E residue 77 THR 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 175 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 178 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.045774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.034410 restraints weight = 94326.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.035634 restraints weight = 51364.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.036433 restraints weight = 35637.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.036942 restraints weight = 28328.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.037294 restraints weight = 24515.371| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14791 Z= 0.097 Angle : 0.598 12.499 19964 Z= 0.279 Chirality : 0.040 0.190 2388 Planarity : 0.004 0.054 2535 Dihedral : 6.704 118.983 2039 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.50 % Allowed : 18.96 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.20), residues: 1838 helix: 1.65 (0.16), residues: 1104 sheet: -0.42 (0.33), residues: 222 loop : 1.04 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 392 TYR 0.016 0.001 TYR D 443 PHE 0.012 0.001 PHE G 408 TRP 0.018 0.001 TRP F 280 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00220 (14791) covalent geometry : angle 0.59774 (19964) hydrogen bonds : bond 0.02574 ( 804) hydrogen bonds : angle 3.54300 ( 2322) ********************** 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 122 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.644 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: 0.8000 (ppp) cc_final: 0.7695 (ppp) REVERT: D 437 MET cc_start: 0.9004 (ttp) cc_final: 0.8707 (ttp) REVERT: C 64 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8174 (tpp) REVERT: C 118 ASN cc_start: 0.9150 (m-40) cc_final: 0.8818 (t0) REVERT: F 84 MET cc_start: 0.8886 (mtm) cc_final: 0.8464 (mpp) REVERT: F 379 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7620 (ppp) REVERT: E 98 MET cc_start: 0.8394 (tpt) cc_final: 0.8187 (tpt) REVERT: E 119 PHE cc_start: 0.9175 (t80) cc_final: 0.8898 (t80) REVERT: G 404 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7524 (t) REVERT: G 440 GLU cc_start: 0.9809 (mp0) cc_final: 0.9528 (pm20) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.1153 time to fit residues: 21.6592 Evaluate side-chains 114 residues out of total 1604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 408 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 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 330 THR Chi-restraints excluded: chain F residue 379 MET Chi-restraints excluded: chain F residue 403 ILE 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 117 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 160 optimal weight: 0.0050 chunk 124 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.043434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.032014 restraints weight = 96662.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.033150 restraints weight = 53434.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.033908 restraints weight = 37465.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.034371 restraints weight = 29969.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.034702 restraints weight = 26103.458| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14791 Z= 0.282 Angle : 0.726 12.047 19964 Z= 0.347 Chirality : 0.042 0.187 2388 Planarity : 0.004 0.057 2535 Dihedral : 6.709 124.512 2039 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.56 % Allowed : 19.21 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.21), residues: 1838 helix: 1.63 (0.16), residues: 1101 sheet: -0.35 (0.33), residues: 214 loop : 0.92 (0.30), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 392 TYR 0.026 0.002 TYR C 317 PHE 0.017 0.002 PHE E 119 TRP 0.017 0.002 TRP F 280 HIS 0.007 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00605 (14791) covalent geometry : angle 0.72600 (19964) hydrogen bonds : bond 0.03264 ( 804) hydrogen bonds : angle 4.02711 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.35 seconds wall clock time: 43 minutes 19.06 seconds (2599.06 seconds total)