Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 06:04:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/04_2023/7z38_14473_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/04_2023/7z38_14473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/04_2023/7z38_14473.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/04_2023/7z38_14473.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/04_2023/7z38_14473_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z38_14473/04_2023/7z38_14473_updated.pdb" } resolution = 3.16 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 74 5.16 5 C 9007 2.51 5 N 2423 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B ASP 422": "OD1" <-> "OD2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ASP 529": "OD1" <-> "OD2" Residue "B TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "C TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C ASP 530": "OD1" <-> "OD2" Residue "C TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14258 Number of models: 1 Model: "" Number of chains: 6 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: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5173 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 17, 'TRANS': 620} Chain breaks: 1 Chain: "C" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1564 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "D" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2299 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.78, per 1000 atoms: 0.55 Number of scatterers: 14258 At special positions: 0 Unit cell: (124.8, 118.976, 152.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 7 15.00 Mg 2 11.99 O 2745 8.00 N 2423 7.00 C 9007 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: 6.14 Conformation dependent library (CDL) restraints added in 2.0 seconds 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 9 sheets defined 45.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 36 through 60 removed outlier: 3.787A pdb=" N PHE A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 57 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 117 removed outlier: 3.848A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 398 through 419 removed outlier: 4.274A pdb=" N VAL A 409 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 443 removed outlier: 6.538A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 3.744A pdb=" N GLU A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.651A pdb=" N GLN A 524 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 562 through 570 Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 614 through 616 No H-bonds generated for 'chain 'A' and resid 614 through 616' Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.615A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 36 through 60 removed outlier: 3.545A pdb=" N LEU B 40 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' 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 400 through 420 Processing helix chain 'B' and resid 423 through 443 removed outlier: 3.992A pdb=" N LYS B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 3.899A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 498 through 505 removed outlier: 3.577A pdb=" N GLU B 501 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 4.153A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 570 removed outlier: 5.362A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 removed outlier: 3.665A pdb=" N ALA B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.659A pdb=" N LYS B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 666 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'C' and resid 442 through 461 removed outlier: 3.660A pdb=" N ILE C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 473 No H-bonds generated for 'chain 'C' and resid 471 through 473' Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 527 through 542 Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.935A pdb=" N ILE C 558 " --> pdb=" O ARG C 554 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 559 " --> pdb=" O ASP C 555 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET C 560 " --> pdb=" O GLN C 556 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 588 Processing helix chain 'C' and resid 599 through 611 removed outlier: 3.528A pdb=" N SER C 604 " --> pdb=" O PRO C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 73 removed outlier: 4.154A pdb=" N ARG D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 111 removed outlier: 3.776A pdb=" N GLU D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 143 through 154 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 184 through 200 Processing helix chain 'D' and resid 203 through 226 removed outlier: 3.892A pdb=" N GLN D 212 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.815A pdb=" N PHE D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG D 235 " --> pdb=" O ARG D 231 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE D 237 " --> pdb=" O CYS D 233 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE D 238 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 273 Processing sheet with id= A, first strand: chain 'A' and resid 165 through 168 removed outlier: 7.108A pdb=" N HIS A 184 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A 143 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 182 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL A 145 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS A 180 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR A 147 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY A 178 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE A 75 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR A 214 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR A 216 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 217 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 360 through 363 removed outlier: 6.905A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 379 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR A 356 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL A 381 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 533 through 535 removed outlier: 5.512A pdb=" N ILE A 483 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 577 through 580 removed outlier: 3.812A pdb=" N LYS A 577 " --> pdb=" O LYS A 624 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 83 through 88 removed outlier: 7.337A pdb=" N ILE B 75 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR B 214 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR B 216 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 217 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 165 through 168 removed outlier: 3.604A pdb=" N ARG B 168 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N HIS B 184 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 143 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 182 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 145 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS B 180 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 147 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B 178 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.856A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 363 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL B 357 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 532 through 535 removed outlier: 6.333A pdb=" N VAL B 511 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 577 through 580 584 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: 4.40 Time building geometry restraints manager: 6.56 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: 4683 1.34 - 1.46: 2716 1.46 - 1.58: 6965 1.58 - 1.69: 11 1.69 - 1.81: 126 Bond restraints: 14501 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 1.619 -0.127 5.00e-02 4.00e+02 6.42e+00 bond pdb=" N VAL B 592 " pdb=" CA VAL B 592 " ideal model delta sigma weight residual 1.454 1.434 0.020 1.28e-02 6.10e+03 2.46e+00 bond pdb=" CG PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 1.503 1.556 -0.053 3.40e-02 8.65e+02 2.42e+00 bond pdb=" CG1 ILE B 591 " pdb=" CD1 ILE B 591 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.01e+00 bond pdb=" CA HIS A 171 " pdb=" C HIS A 171 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.73e+00 ... (remaining 14496 not shown) Histogram of bond angle deviations from ideal: 98.17 - 106.59: 305 106.59 - 115.02: 8835 115.02 - 123.45: 10003 123.45 - 131.87: 324 131.87 - 140.30: 22 Bond angle restraints: 19489 Sorted by residual: angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 102.43 9.57 1.40e+00 5.10e-01 4.68e+01 angle pdb=" C GLU D 142 " pdb=" CA GLU D 142 " pdb=" CB GLU D 142 " ideal model delta sigma weight residual 116.63 109.99 6.64 1.16e+00 7.43e-01 3.28e+01 angle pdb=" CA GLU D 142 " pdb=" C GLU D 142 " pdb=" N VAL D 143 " ideal model delta sigma weight residual 119.63 116.66 2.97 8.10e-01 1.52e+00 1.35e+01 angle pdb=" CA LYS A 349 " pdb=" CB LYS A 349 " pdb=" CG LYS A 349 " ideal model delta sigma weight residual 114.10 119.60 -5.50 2.00e+00 2.50e-01 7.55e+00 angle pdb=" C CYS C 424 " pdb=" N GLU C 425 " pdb=" CA GLU C 425 " ideal model delta sigma weight residual 121.54 126.76 -5.22 1.91e+00 2.74e-01 7.47e+00 ... (remaining 19484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7597 17.98 - 35.97: 977 35.97 - 53.95: 254 53.95 - 71.94: 79 71.94 - 89.92: 37 Dihedral angle restraints: 8944 sinusoidal: 3819 harmonic: 5125 Sorted by residual: dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N GLN B 118 " pdb=" CA GLN B 118 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA A 432 " pdb=" C ALA A 432 " pdb=" N PHE A 433 " pdb=" CA PHE A 433 " ideal model delta harmonic sigma weight residual -180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP A 314 " pdb=" CB ASP A 314 " pdb=" CG ASP A 314 " pdb=" OD1 ASP A 314 " ideal model delta sinusoidal sigma weight residual -30.00 -88.45 58.45 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 8941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1461 0.038 - 0.077: 523 0.077 - 0.115: 127 0.115 - 0.153: 23 0.153 - 0.191: 2 Chirality restraints: 2136 Sorted by residual: chirality pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" C PRO A 79 " pdb=" CB PRO A 79 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU C 603 " pdb=" CB LEU C 603 " pdb=" CD1 LEU C 603 " pdb=" CD2 LEU C 603 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2133 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 78 " 0.066 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO A 79 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 79 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 79 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 32 " 0.021 2.00e-02 2.50e+03 1.76e-02 5.39e+00 pdb=" CG PHE A 32 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 32 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 32 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 32 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 32 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 32 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 280 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C GLU A 280 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU A 280 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 281 " 0.011 2.00e-02 2.50e+03 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 203 2.65 - 3.21: 13318 3.21 - 3.77: 21950 3.77 - 4.34: 30648 4.34 - 4.90: 50811 Nonbonded interactions: 116930 Sorted by model distance: nonbonded pdb=" O ASN A 100 " pdb=" OG1 THR A 104 " model vdw 2.085 2.440 nonbonded pdb=" OH TYR B 520 " pdb=" OE1 GLN B 609 " model vdw 2.137 2.440 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 802 " model vdw 2.138 2.170 nonbonded pdb=" O GLY B 132 " pdb=" OG SER B 135 " model vdw 2.183 2.440 nonbonded pdb=" O GLU B 328 " pdb=" OG SER B 383 " model vdw 2.196 2.440 ... (remaining 116925 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 10 through 690 or resid 801 through 802)) selection = (chain 'B' and (resid 10 through 223 or resid 270 through 690 or resid 801 throu \ gh 802)) } 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=0.00 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: 2.410 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: 13.270 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 38.290 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 0.127 14501 Z= 0.314 Angle : 0.605 9.574 19489 Z= 0.332 Chirality : 0.042 0.191 2136 Planarity : 0.004 0.094 2486 Dihedral : 18.551 89.919 5614 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.08 % Rotamer Outliers : 0.19 % 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: -0.56 (0.21), residues: 1723 helix: 0.82 (0.19), residues: 809 sheet: -1.19 (0.36), residues: 213 loop : -1.50 (0.23), residues: 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 177 average time/residue: 0.3135 time to fit residues: 79.2622 Evaluate side-chains 174 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1589 time to fit residues: 3.4982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 14501 Z= 0.279 Angle : 0.535 7.071 19489 Z= 0.288 Chirality : 0.041 0.156 2136 Planarity : 0.004 0.041 2486 Dihedral : 5.036 58.425 1895 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer Outliers : 3.17 % 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: -0.58 (0.20), residues: 1723 helix: 0.80 (0.19), residues: 792 sheet: -1.10 (0.36), residues: 209 loop : -1.48 (0.23), residues: 722 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 181 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 23 residues processed: 216 average time/residue: 0.2909 time to fit residues: 90.5234 Evaluate side-chains 197 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1662 time to fit residues: 8.7573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.0570 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 GLN D 208 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14501 Z= 0.212 Angle : 0.499 6.883 19489 Z= 0.267 Chirality : 0.040 0.152 2136 Planarity : 0.004 0.040 2486 Dihedral : 4.933 58.186 1895 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.20), residues: 1723 helix: 0.77 (0.19), residues: 794 sheet: -1.01 (0.36), residues: 204 loop : -1.43 (0.23), residues: 725 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 184 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 11 residues processed: 216 average time/residue: 0.2863 time to fit residues: 89.7813 Evaluate side-chains 187 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1361 time to fit residues: 5.2286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 30.0000 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 105 optimal weight: 0.3980 chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14501 Z= 0.193 Angle : 0.496 7.159 19489 Z= 0.263 Chirality : 0.039 0.152 2136 Planarity : 0.004 0.041 2486 Dihedral : 4.850 58.005 1895 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer Outliers : 2.67 % 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: -0.50 (0.21), residues: 1723 helix: 0.79 (0.19), residues: 794 sheet: -0.92 (0.36), residues: 204 loop : -1.39 (0.23), residues: 725 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 13 residues processed: 210 average time/residue: 0.2993 time to fit residues: 90.8084 Evaluate side-chains 183 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1334 time to fit residues: 5.8341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 7.9990 chunk 94 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 14501 Z= 0.326 Angle : 0.567 7.927 19489 Z= 0.298 Chirality : 0.042 0.242 2136 Planarity : 0.004 0.040 2486 Dihedral : 5.105 58.387 1895 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.62 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.70 (0.20), residues: 1723 helix: 0.61 (0.19), residues: 797 sheet: -1.07 (0.36), residues: 212 loop : -1.47 (0.23), residues: 714 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 200 average time/residue: 0.3140 time to fit residues: 91.5051 Evaluate side-chains 186 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1649 time to fit residues: 8.4753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 87 optimal weight: 0.0980 chunk 160 optimal weight: 10.0000 overall best weight: 0.7386 ------------------------------------------------------------------------------- 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 523 GLN D 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14501 Z= 0.214 Angle : 0.506 7.806 19489 Z= 0.267 Chirality : 0.040 0.166 2136 Planarity : 0.004 0.040 2486 Dihedral : 4.940 58.154 1895 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.20 % Rotamer Outliers : 1.40 % 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: -0.58 (0.20), residues: 1723 helix: 0.71 (0.19), residues: 794 sheet: -1.01 (0.36), residues: 204 loop : -1.40 (0.23), residues: 725 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 195 average time/residue: 0.3040 time to fit residues: 85.2550 Evaluate side-chains 177 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1180 time to fit residues: 4.1709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 121 optimal weight: 0.8980 chunk 140 optimal weight: 0.0020 chunk 92 optimal weight: 0.5980 chunk 165 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 GLN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 14501 Z= 0.162 Angle : 0.480 6.729 19489 Z= 0.255 Chirality : 0.039 0.191 2136 Planarity : 0.004 0.040 2486 Dihedral : 4.760 57.453 1895 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer Outliers : 0.89 % 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: -0.50 (0.21), residues: 1723 helix: 0.81 (0.19), residues: 792 sheet: -0.93 (0.36), residues: 204 loop : -1.41 (0.23), residues: 727 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 192 average time/residue: 0.2906 time to fit residues: 80.9454 Evaluate side-chains 177 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1468 time to fit residues: 4.5701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 0.0020 chunk 144 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 523 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14501 Z= 0.210 Angle : 0.515 7.790 19489 Z= 0.271 Chirality : 0.040 0.211 2136 Planarity : 0.004 0.041 2486 Dihedral : 4.813 57.584 1895 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer Outliers : 0.89 % 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: -0.46 (0.20), residues: 1723 helix: 0.88 (0.19), residues: 787 sheet: -0.97 (0.36), residues: 204 loop : -1.40 (0.23), residues: 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 185 average time/residue: 0.3013 time to fit residues: 80.8233 Evaluate side-chains 179 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2266 time to fit residues: 5.2856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 5.9990 chunk 158 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 0.0670 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 50.0000 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- 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** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 14501 Z= 0.234 Angle : 0.532 13.110 19489 Z= 0.277 Chirality : 0.040 0.208 2136 Planarity : 0.004 0.041 2486 Dihedral : 4.868 57.995 1895 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer Outliers : 0.83 % 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: -0.53 (0.20), residues: 1723 helix: 0.81 (0.19), residues: 795 sheet: -0.98 (0.36), residues: 203 loop : -1.44 (0.23), residues: 725 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 179 average time/residue: 0.2996 time to fit residues: 77.3442 Evaluate side-chains 174 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1436 time to fit residues: 4.0346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** D 42 GLN D 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 14501 Z= 0.248 Angle : 0.546 12.749 19489 Z= 0.284 Chirality : 0.041 0.207 2136 Planarity : 0.004 0.040 2486 Dihedral : 4.927 58.407 1895 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.20), residues: 1723 helix: 0.76 (0.19), residues: 795 sheet: -1.05 (0.36), residues: 208 loop : -1.44 (0.23), residues: 720 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 172 average time/residue: 0.3069 time to fit residues: 76.6356 Evaluate side-chains 169 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 165 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1312 time to fit residues: 3.5124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 140 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** D 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.203259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.151906 restraints weight = 15725.521| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.59 r_work: 0.3588 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 14501 Z= 0.201 Angle : 0.522 12.285 19489 Z= 0.272 Chirality : 0.040 0.218 2136 Planarity : 0.004 0.041 2486 Dihedral : 4.867 58.421 1895 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.20 % Rotamer Outliers : 0.13 % 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: -0.49 (0.20), residues: 1723 helix: 0.87 (0.19), residues: 787 sheet: -1.03 (0.36), residues: 209 loop : -1.41 (0.23), residues: 727 =============================================================================== Job complete usr+sys time: 3293.14 seconds wall clock time: 60 minutes 43.34 seconds (3643.34 seconds total)