Starting phenix.real_space_refine (version: dev) on Thu Feb 23 04:06:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2023/6bob_7123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2023/6bob_7123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2023/6bob_7123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2023/6bob_7123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2023/6bob_7123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bob_7123/02_2023/6bob_7123.pdb" } resolution = 3.9 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= 0.001 sd= 0.009 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 Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 588": "NH1" <-> "NH2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 354": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D ARG 614": "NH1" <-> "NH2" Residue "D ARG 635": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Chain: "B" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Chain: "C" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Chain: "D" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4835 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 25, 'TRANS': 577} Chain breaks: 1 Time building chain proxies: 11.18, per 1000 atoms: 0.58 Number of scatterers: 19340 At special positions: 0 Unit cell: (132.3, 132.3, 123.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3436 8.00 N 3244 7.00 C 12524 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 - 3.50 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=0, symmetry=0 Time building additional restraints: 7.79 Conformation dependent library (CDL) restraints added in 3.2 seconds 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 59.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.831A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.574A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.902A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.530A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.730A pdb=" N GLY A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 290 through 296 removed outlier: 3.688A pdb=" N VAL A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE A 306 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 315 " --> pdb=" O PRO A 311 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR A 323 " --> pdb=" O LYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 348 removed outlier: 3.599A pdb=" N TYR A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 424 through 442 removed outlier: 3.675A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG A 469 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.592A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY A 502 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 607 removed outlier: 3.554A pdb=" N LEU A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.831A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.573A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.683A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.729A pdb=" N GLY B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.688A pdb=" N VAL B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.598A pdb=" N ILE B 306 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 336 " --> pdb=" O GLY B 332 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 408 through 410 No H-bonds generated for 'chain 'B' and resid 408 through 410' Processing helix chain 'B' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG B 469 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.593A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 484 " --> pdb=" O MET B 480 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP B 494 " --> pdb=" O MET B 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 563 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.830A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.573A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.730A pdb=" N GLY C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.689A pdb=" N VAL C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE C 306 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR C 323 " --> pdb=" O LYS C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 435 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 463 removed outlier: 3.573A pdb=" N VAL C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 469 removed outlier: 3.525A pdb=" N ARG C 469 " --> pdb=" O TYR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 486 removed outlier: 3.592A pdb=" N THR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET C 484 " --> pdb=" O MET C 480 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP C 494 " --> pdb=" O MET C 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY C 502 " --> pdb=" O VAL C 498 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 524 through 537 removed outlier: 3.546A pdb=" N ALA C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 579 removed outlier: 3.603A pdb=" N SER C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 563 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 570 " --> pdb=" O THR C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 removed outlier: 3.830A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.574A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.901A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 171 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.682A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.532A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.729A pdb=" N GLY D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.689A pdb=" N VAL D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.597A pdb=" N ILE D 306 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 324 removed outlier: 3.654A pdb=" N GLU D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR D 323 " --> pdb=" O LYS D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 348 removed outlier: 3.598A pdb=" N TYR D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 336 " --> pdb=" O GLY D 332 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS D 345 " --> pdb=" O CYS D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 407 removed outlier: 3.622A pdb=" N VAL D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 396 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'D' and resid 408 through 410 No H-bonds generated for 'chain 'D' and resid 408 through 410' Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.676A pdb=" N VAL D 429 " --> pdb=" O HIS D 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 435 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 463 removed outlier: 3.574A pdb=" N VAL D 458 " --> pdb=" O SER D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.524A pdb=" N ARG D 469 " --> pdb=" O TYR D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 486 removed outlier: 3.593A pdb=" N THR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 480 " --> pdb=" O PRO D 476 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 511 removed outlier: 4.231A pdb=" N TRP D 494 " --> pdb=" O MET D 490 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY D 502 " --> pdb=" O VAL D 498 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 524 through 537 removed outlier: 3.545A pdb=" N ALA D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 579 removed outlier: 3.602A pdb=" N SER D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 570 " --> pdb=" O THR D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 607 removed outlier: 3.553A pdb=" N LEU D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE A 265 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 276 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE B 265 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU B 276 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE C 265 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU C 276 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 263 through 269 removed outlier: 4.726A pdb=" N ILE D 265 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU D 276 " --> pdb=" O ILE D 265 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2436 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: 5.51 Time building geometry restraints manager: 8.45 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: 6065 1.34 - 1.46: 3828 1.46 - 1.57: 9667 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 19788 Sorted by residual: bond pdb=" C ASP C 515 " pdb=" N PRO C 516 " ideal model delta sigma weight residual 1.337 1.309 0.027 1.06e-02 8.90e+03 6.68e+00 bond pdb=" C ASP D 515 " pdb=" N PRO D 516 " ideal model delta sigma weight residual 1.337 1.309 0.027 1.06e-02 8.90e+03 6.53e+00 bond pdb=" C ASP A 515 " pdb=" N PRO A 516 " ideal model delta sigma weight residual 1.337 1.310 0.027 1.06e-02 8.90e+03 6.43e+00 bond pdb=" C ASP B 515 " pdb=" N PRO B 516 " ideal model delta sigma weight residual 1.337 1.310 0.026 1.06e-02 8.90e+03 6.13e+00 bond pdb=" N ASN D 357 " pdb=" CA ASN D 357 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.70e+00 ... (remaining 19783 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.44: 420 105.44 - 112.88: 10407 112.88 - 120.33: 8382 120.33 - 127.78: 7425 127.78 - 135.23: 234 Bond angle restraints: 26868 Sorted by residual: angle pdb=" N CYS B 610 " pdb=" CA CYS B 610 " pdb=" C CYS B 610 " ideal model delta sigma weight residual 114.56 106.24 8.32 1.27e+00 6.20e-01 4.29e+01 angle pdb=" N CYS C 610 " pdb=" CA CYS C 610 " pdb=" C CYS C 610 " ideal model delta sigma weight residual 114.56 106.27 8.29 1.27e+00 6.20e-01 4.26e+01 angle pdb=" N CYS D 610 " pdb=" CA CYS D 610 " pdb=" C CYS D 610 " ideal model delta sigma weight residual 114.56 106.28 8.28 1.27e+00 6.20e-01 4.25e+01 angle pdb=" N CYS A 610 " pdb=" CA CYS A 610 " pdb=" C CYS A 610 " ideal model delta sigma weight residual 114.56 106.29 8.27 1.27e+00 6.20e-01 4.24e+01 angle pdb=" CA LEU C 228 " pdb=" CB LEU C 228 " pdb=" CG LEU C 228 " ideal model delta sigma weight residual 116.30 135.23 -18.93 3.50e+00 8.16e-02 2.93e+01 ... (remaining 26863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 10894 15.61 - 31.21: 672 31.21 - 46.82: 182 46.82 - 62.42: 20 62.42 - 78.03: 12 Dihedral angle restraints: 11780 sinusoidal: 4732 harmonic: 7048 Sorted by residual: dihedral pdb=" CA ARG B 354 " pdb=" C ARG B 354 " pdb=" N ILE B 355 " pdb=" CA ILE B 355 " ideal model delta harmonic sigma weight residual 180.00 -132.20 -47.80 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA ARG C 354 " pdb=" C ARG C 354 " pdb=" N ILE C 355 " pdb=" CA ILE C 355 " ideal model delta harmonic sigma weight residual -180.00 -132.25 -47.75 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA ARG D 354 " pdb=" C ARG D 354 " pdb=" N ILE D 355 " pdb=" CA ILE D 355 " ideal model delta harmonic sigma weight residual -180.00 -132.25 -47.75 0 5.00e+00 4.00e-02 9.12e+01 ... (remaining 11777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2089 0.054 - 0.107: 739 0.107 - 0.161: 182 0.161 - 0.215: 30 0.215 - 0.268: 16 Chirality restraints: 3056 Sorted by residual: chirality pdb=" CA THR D 310 " pdb=" N THR D 310 " pdb=" C THR D 310 " pdb=" CB THR D 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA THR A 310 " pdb=" N THR A 310 " pdb=" C THR A 310 " pdb=" CB THR A 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA THR C 310 " pdb=" N THR C 310 " pdb=" C THR C 310 " pdb=" CB THR C 310 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3053 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 354 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ARG D 354 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG D 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE D 355 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 354 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ARG C 354 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG C 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE C 355 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 354 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ARG B 354 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG B 354 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE B 355 " 0.021 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5012 2.79 - 3.32: 18582 3.32 - 3.84: 32030 3.84 - 4.37: 37973 4.37 - 4.90: 61282 Nonbonded interactions: 154879 Sorted by model distance: nonbonded pdb=" OH TYR C 323 " pdb=" O PRO C 613 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR D 323 " pdb=" O PRO D 613 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR A 323 " pdb=" O PRO A 613 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR B 323 " pdb=" O PRO B 613 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR C 338 " pdb=" O SER C 391 " model vdw 2.274 2.440 ... (remaining 154874 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 12524 2.51 5 N 3244 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.670 Check model and map are aligned: 0.280 Process input model: 49.490 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 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 0.117 19788 Z= 0.431 Angle : 1.198 18.931 26868 Z= 0.634 Chirality : 0.060 0.268 3056 Planarity : 0.007 0.067 3396 Dihedral : 11.836 78.026 7236 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.14 % Favored : 88.52 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -4.96 (0.13), residues: 2396 helix: -3.23 (0.09), residues: 1292 sheet: -0.70 (0.59), residues: 76 loop : -3.48 (0.17), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 714 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 724 average time/residue: 0.3201 time to fit residues: 343.2113 Evaluate side-chains 406 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 399 time to evaluate : 2.021 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1799 time to fit residues: 5.6438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 0.2980 chunk 188 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 0.0670 chunk 217 optimal weight: 0.0980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 118 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN A 217 ASN A 227 HIS A 257 HIS A 309 GLN A 357 ASN A 360 ASN A 463 ASN B 37 ASN B 40 GLN B 118 GLN ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 206 GLN B 208 ASN B 217 ASN B 227 HIS B 257 HIS B 309 GLN B 360 ASN B 445 ASN B 463 ASN B 571 ASN C 40 GLN C 118 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 217 ASN C 227 HIS C 251 ASN C 257 HIS C 360 ASN C 463 ASN C 571 ASN D 40 GLN D 96 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 HIS D 208 ASN D 217 ASN D 227 HIS D 251 ASN D 257 HIS D 357 ASN D 360 ASN D 463 ASN D 512 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19788 Z= 0.179 Angle : 0.722 8.900 26868 Z= 0.360 Chirality : 0.043 0.173 3056 Planarity : 0.005 0.039 3396 Dihedral : 5.866 43.653 2636 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.47 % Favored : 93.36 % Rotamer Outliers : 4.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.89 (0.15), residues: 2396 helix: -1.12 (0.12), residues: 1384 sheet: -0.35 (0.57), residues: 84 loop : -3.30 (0.18), residues: 928 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 481 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 32 residues processed: 541 average time/residue: 0.2942 time to fit residues: 244.8717 Evaluate side-chains 426 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 394 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1732 time to fit residues: 13.7355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 445 ASN A 463 ASN A 521 HIS B 84 HIS ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 HIS B 463 ASN B 521 HIS B 571 ASN B 595 GLN C 40 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 521 HIS C 571 ASN C 595 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 425 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 19788 Z= 0.282 Angle : 0.755 12.499 26868 Z= 0.380 Chirality : 0.046 0.215 3056 Planarity : 0.004 0.037 3396 Dihedral : 5.533 43.521 2636 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.01 % Favored : 91.82 % Rotamer Outliers : 4.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.10 (0.16), residues: 2396 helix: -0.38 (0.14), residues: 1360 sheet: -0.35 (0.55), residues: 84 loop : -3.03 (0.19), residues: 952 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 444 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 42 residues processed: 519 average time/residue: 0.2952 time to fit residues: 238.3194 Evaluate side-chains 396 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 354 time to evaluate : 2.328 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1796 time to fit residues: 17.1300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN A 521 HIS ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN B 521 HIS C 40 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 463 ASN D 40 GLN ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 521 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 19788 Z= 0.305 Angle : 0.762 11.973 26868 Z= 0.378 Chirality : 0.046 0.265 3056 Planarity : 0.004 0.057 3396 Dihedral : 5.373 40.030 2636 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.10 % Favored : 91.74 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.84 (0.17), residues: 2396 helix: -0.19 (0.14), residues: 1372 sheet: -1.02 (0.51), residues: 84 loop : -2.84 (0.19), residues: 940 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 391 time to evaluate : 2.327 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 30 residues processed: 438 average time/residue: 0.3089 time to fit residues: 209.4714 Evaluate side-chains 372 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 342 time to evaluate : 2.113 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1819 time to fit residues: 13.5040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 208 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 463 ASN B 40 GLN B 96 GLN B 425 HIS B 463 ASN B 521 HIS B 571 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN D 84 HIS D 463 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 19788 Z= 0.274 Angle : 0.747 11.933 26868 Z= 0.368 Chirality : 0.046 0.239 3056 Planarity : 0.004 0.045 3396 Dihedral : 5.263 36.090 2636 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.43 % Favored : 91.53 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.69 (0.17), residues: 2396 helix: 0.03 (0.14), residues: 1360 sheet: -1.30 (0.49), residues: 84 loop : -2.86 (0.19), residues: 952 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 396 time to evaluate : 2.278 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 18 residues processed: 433 average time/residue: 0.3035 time to fit residues: 202.4392 Evaluate side-chains 370 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 352 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1720 time to fit residues: 8.7094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 40 GLN B 96 GLN B 122 HIS B 463 ASN C 40 GLN C 96 GLN C 206 GLN C 305 GLN C 463 ASN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 512 GLN D 521 HIS ** D 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19788 Z= 0.196 Angle : 0.720 12.539 26868 Z= 0.348 Chirality : 0.044 0.306 3056 Planarity : 0.004 0.045 3396 Dihedral : 4.995 32.295 2636 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.51 (0.17), residues: 2396 helix: 0.15 (0.14), residues: 1372 sheet: -0.26 (0.53), residues: 64 loop : -2.83 (0.19), residues: 960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 397 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 15 residues processed: 429 average time/residue: 0.2968 time to fit residues: 200.0767 Evaluate side-chains 380 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 365 time to evaluate : 2.272 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1886 time to fit residues: 8.3874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 373 GLN A 445 ASN A 463 ASN B 463 ASN C 463 ASN D 118 GLN D 128 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19788 Z= 0.184 Angle : 0.744 13.857 26868 Z= 0.353 Chirality : 0.045 0.335 3056 Planarity : 0.004 0.040 3396 Dihedral : 4.821 27.830 2636 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 1.58 % 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: -1.48 (0.17), residues: 2396 helix: 0.23 (0.14), residues: 1364 sheet: -0.37 (0.53), residues: 64 loop : -2.88 (0.19), residues: 968 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 410 time to evaluate : 2.032 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 10 residues processed: 426 average time/residue: 0.2966 time to fit residues: 197.2922 Evaluate side-chains 377 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 367 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2162 time to fit residues: 6.8685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 138 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 114 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 214 GLN B 463 ASN B 581 HIS C 40 GLN C 122 HIS C 214 GLN C 305 GLN C 369 GLN C 463 ASN D 214 GLN D 305 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 19788 Z= 0.181 Angle : 0.758 14.843 26868 Z= 0.353 Chirality : 0.044 0.243 3056 Planarity : 0.004 0.037 3396 Dihedral : 4.679 23.878 2636 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.17), residues: 2396 helix: 0.31 (0.14), residues: 1364 sheet: -0.43 (0.52), residues: 64 loop : -2.83 (0.19), residues: 968 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 397 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 410 average time/residue: 0.2855 time to fit residues: 185.6427 Evaluate side-chains 383 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 373 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1780 time to fit residues: 6.5513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 202 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 463 ASN B 40 GLN B 463 ASN B 581 HIS C 463 ASN D 128 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 19788 Z= 0.198 Angle : 0.777 12.815 26868 Z= 0.363 Chirality : 0.045 0.305 3056 Planarity : 0.004 0.036 3396 Dihedral : 4.664 20.324 2636 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 0.67 % 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: -1.41 (0.17), residues: 2396 helix: 0.25 (0.14), residues: 1376 sheet: -0.50 (0.52), residues: 64 loop : -2.82 (0.19), residues: 956 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 392 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 400 average time/residue: 0.2973 time to fit residues: 184.9358 Evaluate side-chains 374 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 369 time to evaluate : 2.336 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1779 time to fit residues: 4.9314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 463 ASN A 521 HIS B 463 ASN B 581 HIS C 84 HIS C 305 GLN C 463 ASN D 305 GLN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 19788 Z= 0.272 Angle : 0.824 13.442 26868 Z= 0.390 Chirality : 0.047 0.369 3056 Planarity : 0.004 0.036 3396 Dihedral : 4.915 20.375 2636 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.17), residues: 2396 helix: 0.17 (0.14), residues: 1376 sheet: -0.78 (0.50), residues: 64 loop : -2.73 (0.19), residues: 956 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4792 Ramachandran restraints generated. 2396 Oldfield, 0 Emsley, 2396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 375 time to evaluate : 2.292 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 380 average time/residue: 0.3058 time to fit residues: 180.0167 Evaluate side-chains 373 residues out of total 2092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 364 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1833 time to fit residues: 6.3243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 463 ASN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS ** B 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 463 ASN ** D 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN D 595 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116140 restraints weight = 32496.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.118359 restraints weight = 21539.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120076 restraints weight = 16672.811| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 19788 Z= 0.252 Angle : 0.811 12.118 26868 Z= 0.386 Chirality : 0.046 0.270 3056 Planarity : 0.004 0.035 3396 Dihedral : 4.931 20.918 2636 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer Outliers : 0.76 % 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: -1.37 (0.17), residues: 2396 helix: 0.25 (0.14), residues: 1356 sheet: -0.89 (0.50), residues: 64 loop : -2.64 (0.19), residues: 976 =============================================================================== Job complete usr+sys time: 4099.84 seconds wall clock time: 74 minutes 52.61 seconds (4492.61 seconds total)