Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 19:51:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/04_2023/8h77_34519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/04_2023/8h77_34519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/04_2023/8h77_34519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/04_2023/8h77_34519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/04_2023/8h77_34519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/04_2023/8h77_34519_updated.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.004 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 76 5.16 5 Be 2 3.05 5 C 9939 2.51 5 N 2698 2.21 5 O 3001 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E GLU 384": "OE1" <-> "OE2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E GLU 404": "OE1" <-> "OE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 310": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15726 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5158 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 1 Chain: "B" Number of atoms: 5012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5012 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 17, 'TRANS': 602} Chain breaks: 1 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 942 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 928 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "E" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1134 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "F" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2490 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.15, per 1000 atoms: 0.52 Number of scatterers: 15726 At special positions: 0 Unit cell: (113.42, 142.31, 138.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 76 16.00 P 4 15.00 F 6 9.00 O 3001 8.00 N 2698 7.00 C 9939 6.00 Be 2 4.00 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 2.4 seconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 15 sheets defined 34.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 38 through 60 removed outlier: 4.171A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.511A pdb=" N TYR A 137 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 398 through 421 Processing helix chain 'A' and resid 423 through 443 removed outlier: 4.218A pdb=" N LYS A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.746A pdb=" N GLU A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG A 502 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 549 through 570 removed outlier: 4.932A pdb=" N ASN A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 removed outlier: 3.616A pdb=" N ARG A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 removed outlier: 4.285A pdb=" N GLY A 618 " --> pdb=" O SER A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.753A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 4.086A pdb=" N LEU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 38 through 59 Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.716A pdb=" N LEU B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.607A pdb=" N ALA B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 399 through 421 removed outlier: 3.610A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 4.331A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 451 No H-bonds generated for 'chain 'B' and resid 448 through 451' Processing helix chain 'B' and resid 470 through 475 Processing helix chain 'B' and resid 491 through 494 No H-bonds generated for 'chain 'B' and resid 491 through 494' Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 516 through 525 removed outlier: 4.165A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 558 removed outlier: 3.693A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'B' and resid 600 through 608 removed outlier: 4.270A pdb=" N ALA B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 620 removed outlier: 3.552A pdb=" N MET B 617 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 618 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 619 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.791A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.690A pdb=" N LEU E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 321 through 324 No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 328 through 336 removed outlier: 4.119A pdb=" N ARG E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 390 Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'F' and resid 3 through 9 Processing helix chain 'F' and resid 71 through 79 removed outlier: 3.554A pdb=" N CYS F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 108 removed outlier: 3.571A pdb=" N SER F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 143 Processing helix chain 'F' and resid 173 through 192 Proline residue: F 180 - end of helix Processing helix chain 'F' and resid 196 through 215 removed outlier: 4.075A pdb=" N LYS F 215 " --> pdb=" O ASN F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 244 Proline residue: F 232 - end of helix removed outlier: 3.685A pdb=" N CYS F 240 " --> pdb=" O ASN F 236 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS F 241 " --> pdb=" O TYR F 237 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU F 242 " --> pdb=" O CYS F 238 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 259 removed outlier: 3.876A pdb=" N ASN F 259 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 removed outlier: 4.593A pdb=" N ARG F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 294 removed outlier: 3.516A pdb=" N LYS F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 319 Processing helix chain 'F' and resid 321 through 328 removed outlier: 3.772A pdb=" N PHE F 324 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 325 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY F 326 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE F 328 " --> pdb=" O ARG F 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.777A pdb=" N LEU A 217 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR A 216 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE A 75 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 83 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.757A pdb=" N ARG A 221 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU A 274 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS A 223 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE A 272 " --> pdb=" O LYS A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 360 through 363 removed outlier: 7.105A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS A 354 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY A 379 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N TYR A 356 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 381 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 532 through 535 Processing sheet with id= E, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.527A pdb=" N THR B 179 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 360 through 363 removed outlier: 7.130A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LYS B 354 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY B 379 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR B 356 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 381 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 335 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 533 through 535 removed outlier: 5.893A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 577 through 580 removed outlier: 3.985A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS B 590 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.817A pdb=" N ALA C 6 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.123A pdb=" N PHE C 47 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 99 through 101 removed outlier: 6.250A pdb=" N ALA D 6 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.504A pdb=" N HIS D 49 " --> pdb=" O CYS D 40 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 42 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 47 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 291 through 294 removed outlier: 6.307A pdb=" N LYS E 284 " --> pdb=" O ILE E 292 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N CYS E 294 " --> pdb=" O ARG E 282 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ARG E 282 " --> pdb=" O CYS E 294 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE E 364 " --> pdb=" O ASP E 371 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE E 373 " --> pdb=" O ARG E 362 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG E 362 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA E 375 " --> pdb=" O ASN E 360 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN E 360 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN E 377 " --> pdb=" O GLN E 358 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN E 358 " --> pdb=" O GLN E 377 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP E 356 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 355 " --> pdb=" O LEU E 347 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 39 through 41 Processing sheet with id= O, first strand: chain 'F' and resid 34 through 36 removed outlier: 3.646A pdb=" N THR F 35 " --> pdb=" O LYS F 156 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2702 1.32 - 1.44: 4056 1.44 - 1.57: 9132 1.57 - 1.69: 8 1.69 - 1.82: 121 Bond restraints: 16019 Sorted by residual: bond pdb=" CA ASP D 70 " pdb=" C ASP D 70 " ideal model delta sigma weight residual 1.520 1.421 0.099 1.25e-02 6.40e+03 6.29e+01 bond pdb=" CA ASP B 672 " pdb=" C ASP B 672 " ideal model delta sigma weight residual 1.531 1.572 -0.040 7.40e-03 1.83e+04 2.97e+01 bond pdb=" N ARG D 71 " pdb=" CA ARG D 71 " ideal model delta sigma weight residual 1.458 1.389 0.069 1.33e-02 5.65e+03 2.66e+01 bond pdb=" CA THR C 69 " pdb=" C THR C 69 " ideal model delta sigma weight residual 1.526 1.459 0.067 1.37e-02 5.33e+03 2.40e+01 bond pdb=" BE BEF A 802 " pdb=" F2 BEF A 802 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.83e+01 ... (remaining 16014 not shown) Histogram of bond angle deviations from ideal: 96.49 - 104.42: 209 104.42 - 112.36: 7972 112.36 - 120.29: 6960 120.29 - 128.22: 6309 128.22 - 136.16: 114 Bond angle restraints: 21564 Sorted by residual: angle pdb=" C LYS D 65 " pdb=" CA LYS D 65 " pdb=" CB LYS D 65 " ideal model delta sigma weight residual 110.62 100.83 9.79 1.86e+00 2.89e-01 2.77e+01 angle pdb=" N LEU E 325 " pdb=" CA LEU E 325 " pdb=" C LEU E 325 " ideal model delta sigma weight residual 112.89 106.74 6.15 1.24e+00 6.50e-01 2.46e+01 angle pdb=" C1' ADP B 801 " pdb=" C2' ADP B 801 " pdb=" C3' ADP B 801 " ideal model delta sigma weight residual 111.00 96.59 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 112.55 118.69 -6.14 1.35e+00 5.49e-01 2.07e+01 angle pdb=" N CYS E 327 " pdb=" CA CYS E 327 " pdb=" C CYS E 327 " ideal model delta sigma weight residual 112.90 107.20 5.70 1.31e+00 5.83e-01 1.90e+01 ... (remaining 21559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 9462 31.16 - 62.33: 325 62.33 - 93.49: 28 93.49 - 124.65: 0 124.65 - 155.82: 3 Dihedral angle restraints: 9818 sinusoidal: 4156 harmonic: 5662 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 144.19 155.82 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 94.96 -154.96 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 79.51 -139.51 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 9815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2208 0.095 - 0.189: 139 0.189 - 0.284: 6 0.284 - 0.378: 1 0.378 - 0.473: 1 Chirality restraints: 2355 Sorted by residual: chirality pdb=" CA ILE E 374 " pdb=" N ILE E 374 " pdb=" C ILE E 374 " pdb=" CB ILE E 374 " both_signs ideal model delta sigma weight residual False 2.43 2.91 -0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CA THR C 69 " pdb=" N THR C 69 " pdb=" C THR C 69 " pdb=" CB THR C 69 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' ADP B 801 " pdb=" C1' ADP B 801 " pdb=" C3' ADP B 801 " pdb=" O2' ADP B 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2352 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 78 " 0.047 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO B 79 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 396 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO E 397 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 397 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 397 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 285 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C HIS E 285 " 0.033 2.00e-02 2.50e+03 pdb=" O HIS E 285 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS E 286 " -0.011 2.00e-02 2.50e+03 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 3 2.07 - 2.78: 3363 2.78 - 3.49: 21704 3.49 - 4.19: 35327 4.19 - 4.90: 61950 Nonbonded interactions: 122347 Sorted by model distance: nonbonded pdb=" OD1 ASN B 46 " pdb=" F1 BEF B 802 " model vdw 1.365 2.390 nonbonded pdb=" CE LYS E 286 " pdb=" CG2 ILE E 292 " model vdw 1.866 3.860 nonbonded pdb=" OG1 THR E 381 " pdb=" OE1 GLU E 384 " model vdw 2.063 2.440 nonbonded pdb=" NE2 GLN F 315 " pdb=" OE2 GLU F 319 " model vdw 2.096 2.520 nonbonded pdb=" O2' ADP B 801 " pdb=" O3' ADP B 801 " model vdw 2.106 2.432 ... (remaining 122342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 217 or resid 278 through 690 or resid 801 throu \ gh 802)) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 1 through 111) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.820 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 39.200 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 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 : 0.005 0.099 16019 Z= 0.329 Angle : 0.839 14.411 21564 Z= 0.473 Chirality : 0.050 0.473 2355 Planarity : 0.004 0.069 2764 Dihedral : 15.363 155.815 6142 Min Nonbonded Distance : 1.365 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 1912 helix: -0.22 (0.20), residues: 684 sheet: -0.39 (0.29), residues: 325 loop : -1.94 (0.18), residues: 903 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 420 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 421 average time/residue: 0.3560 time to fit residues: 207.4494 Evaluate side-chains 229 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS E 299 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 16019 Z= 0.232 Angle : 0.638 8.559 21564 Z= 0.333 Chirality : 0.045 0.178 2355 Planarity : 0.004 0.048 2764 Dihedral : 7.242 134.495 2115 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.19), residues: 1912 helix: 0.02 (0.20), residues: 686 sheet: 0.13 (0.29), residues: 334 loop : -1.75 (0.19), residues: 892 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 252 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 274 average time/residue: 0.3354 time to fit residues: 130.5691 Evaluate side-chains 228 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1824 time to fit residues: 8.5033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 145 optimal weight: 0.0970 chunk 118 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 188 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 173 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN D 97 ASN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 16019 Z= 0.151 Angle : 0.563 7.603 21564 Z= 0.292 Chirality : 0.042 0.161 2355 Planarity : 0.004 0.048 2764 Dihedral : 6.288 115.690 2115 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1912 helix: 0.24 (0.20), residues: 693 sheet: 0.36 (0.29), residues: 335 loop : -1.55 (0.19), residues: 884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 245 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 260 average time/residue: 0.3163 time to fit residues: 118.4035 Evaluate side-chains 219 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1490 time to fit residues: 5.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 0.0770 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 175 optimal weight: 0.0170 chunk 185 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN D 97 ASN D 104 ASN F 146 GLN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16019 Z= 0.177 Angle : 0.554 7.305 21564 Z= 0.288 Chirality : 0.042 0.163 2355 Planarity : 0.004 0.048 2764 Dihedral : 6.164 116.541 2115 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1912 helix: 0.29 (0.20), residues: 700 sheet: 0.41 (0.30), residues: 318 loop : -1.50 (0.19), residues: 894 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 209 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 229 average time/residue: 0.3109 time to fit residues: 103.2835 Evaluate side-chains 211 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1673 time to fit residues: 7.6536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN B 30 ASN C 97 ASN D 104 ASN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 16019 Z= 0.458 Angle : 0.751 9.549 21564 Z= 0.389 Chirality : 0.050 0.237 2355 Planarity : 0.005 0.052 2764 Dihedral : 7.426 145.847 2115 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 1912 helix: -0.13 (0.20), residues: 682 sheet: 0.15 (0.29), residues: 321 loop : -1.57 (0.19), residues: 909 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 208 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 26 residues processed: 238 average time/residue: 0.3208 time to fit residues: 109.7954 Evaluate side-chains 205 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.922 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1640 time to fit residues: 10.3100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN E 326 HIS E 358 GLN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 16019 Z= 0.178 Angle : 0.584 8.011 21564 Z= 0.302 Chirality : 0.043 0.326 2355 Planarity : 0.004 0.048 2764 Dihedral : 6.554 128.503 2115 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.19), residues: 1912 helix: -0.05 (0.20), residues: 703 sheet: 0.29 (0.29), residues: 313 loop : -1.48 (0.19), residues: 896 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 214 average time/residue: 0.3461 time to fit residues: 105.8291 Evaluate side-chains 193 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2046 time to fit residues: 6.7182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 0.0050 chunk 185 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16019 Z= 0.167 Angle : 0.562 9.587 21564 Z= 0.290 Chirality : 0.042 0.173 2355 Planarity : 0.004 0.047 2764 Dihedral : 6.169 119.711 2115 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1912 helix: 0.11 (0.20), residues: 705 sheet: 0.25 (0.29), residues: 321 loop : -1.37 (0.20), residues: 886 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 212 average time/residue: 0.3329 time to fit residues: 101.7877 Evaluate side-chains 195 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1800 time to fit residues: 5.7744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 6.9990 chunk 110 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN F 213 GLN ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 16019 Z= 0.220 Angle : 0.589 9.193 21564 Z= 0.303 Chirality : 0.043 0.187 2355 Planarity : 0.004 0.047 2764 Dihedral : 6.335 123.084 2115 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1912 helix: 0.14 (0.20), residues: 696 sheet: 0.33 (0.29), residues: 315 loop : -1.35 (0.20), residues: 901 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 204 average time/residue: 0.3293 time to fit residues: 97.3413 Evaluate side-chains 193 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1507 time to fit residues: 4.1446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 103 optimal weight: 0.0030 chunk 75 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 163 optimal weight: 0.0030 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 16019 Z= 0.151 Angle : 0.551 9.171 21564 Z= 0.282 Chirality : 0.042 0.206 2355 Planarity : 0.003 0.047 2764 Dihedral : 5.946 113.414 2115 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1912 helix: 0.22 (0.20), residues: 705 sheet: 0.36 (0.29), residues: 324 loop : -1.25 (0.20), residues: 883 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 202 average time/residue: 0.3290 time to fit residues: 96.1755 Evaluate side-chains 191 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1700 time to fit residues: 3.8579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 16019 Z= 0.395 Angle : 0.712 9.463 21564 Z= 0.366 Chirality : 0.049 0.239 2355 Planarity : 0.005 0.052 2764 Dihedral : 7.074 140.627 2115 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 1912 helix: -0.04 (0.20), residues: 690 sheet: 0.27 (0.29), residues: 315 loop : -1.45 (0.19), residues: 907 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 195 time to evaluate : 2.167 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 198 average time/residue: 0.3392 time to fit residues: 97.1875 Evaluate side-chains 195 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1444 time to fit residues: 3.5822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 152 optimal weight: 0.0270 chunk 63 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.194291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155278 restraints weight = 19376.412| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.79 r_work: 0.3619 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16019 Z= 0.221 Angle : 0.607 8.794 21564 Z= 0.312 Chirality : 0.044 0.183 2355 Planarity : 0.004 0.051 2764 Dihedral : 6.526 124.063 2115 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1912 helix: -0.00 (0.20), residues: 701 sheet: 0.30 (0.30), residues: 313 loop : -1.44 (0.19), residues: 898 =============================================================================== Job complete usr+sys time: 3474.04 seconds wall clock time: 64 minutes 12.14 seconds (3852.14 seconds total)