Starting phenix.real_space_refine on Thu Feb 5 03:09:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njd_49480/02_2026/9njd_49480.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njd_49480/02_2026/9njd_49480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9njd_49480/02_2026/9njd_49480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njd_49480/02_2026/9njd_49480.map" model { file = "/net/cci-nas-00/data/ceres_data/9njd_49480/02_2026/9njd_49480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njd_49480/02_2026/9njd_49480.cif" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 60 5.16 5 C 9066 2.51 5 N 2447 2.21 5 O 2783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14359 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4777 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 31, 'TRANS': 590} Chain breaks: 1 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "B" Number of atoms: 4779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4779 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 31, 'TRANS': 591} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.83, per 1000 atoms: 0.27 Number of scatterers: 14359 At special positions: 0 Unit cell: (107.865, 108.658, 107.865, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 3 15.00 O 2783 8.00 N 2447 7.00 C 9066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 675.9 milliseconds 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3482 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 15 sheets defined 43.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 164 through 180 removed outlier: 4.335A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.785A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 237 through 266 removed outlier: 3.738A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 5.801A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.645A pdb=" N GLU C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 3.571A pdb=" N ILE C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 Processing helix chain 'C' and resid 408 through 416 removed outlier: 3.989A pdb=" N ILE C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.510A pdb=" N ALA C 488 " --> pdb=" O SER C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 540 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.596A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 4.430A pdb=" N ALA C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 653 through 669 removed outlier: 3.519A pdb=" N ILE C 667 " --> pdb=" O PHE C 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.009A pdb=" N LEU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 237 through 267 removed outlier: 3.742A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 6.055A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 removed outlier: 3.666A pdb=" N GLN A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.576A pdb=" N ILE A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 4.012A pdb=" N ILE A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 568 through 593 removed outlier: 3.680A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.235A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.649A pdb=" N SER B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.734A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 255 " --> pdb=" O TYR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 5.505A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 removed outlier: 3.610A pdb=" N GLU B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.805A pdb=" N VAL B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.650A pdb=" N GLY B 405 " --> pdb=" O LEU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 417 removed outlier: 3.733A pdb=" N ASN B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 482 through 499 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 568 through 593 removed outlier: 3.664A pdb=" N LYS B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 4.002A pdb=" N ALA B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 636 Processing helix chain 'B' and resid 653 through 667 removed outlier: 3.636A pdb=" N ALA B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 662 " --> pdb=" O HIS B 658 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.358A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 156 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 199 through 202 removed outlier: 4.029A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASN C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA C 231 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 217 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU C 229 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 219 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 370 through 371 removed outlier: 6.212A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.333A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 156 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 202 removed outlier: 4.139A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 548 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 557 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS A 546 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA A 559 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP A 544 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP A 526 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 200 through 202 removed outlier: 4.139A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.317A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET A 424 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N SER A 474 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS A 426 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL A 476 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU A 428 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLU A 478 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AB2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.336A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 154 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 103 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 156 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.058A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA B 510 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR B 531 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLY B 512 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU B 529 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 514 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B 527 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS B 516 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.058A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.467A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 606 through 611 857 hydrogen bonds defined for protein. 2400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.59 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: 4776 1.34 - 1.46: 2549 1.46 - 1.58: 7165 1.58 - 1.70: 0 1.70 - 1.82: 99 Bond restraints: 14589 Sorted by residual: bond pdb=" CG HIS B 450 " pdb=" CD2 HIS B 450 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.39e+00 bond pdb=" N HIS B 450 " pdb=" CA HIS B 450 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.25e-02 6.40e+03 5.08e+00 bond pdb=" C HIS B 450 " pdb=" O HIS B 450 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.25e-02 6.40e+03 2.05e+00 bond pdb=" CB GLU C 330 " pdb=" CG GLU C 330 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" CB GLU A 330 " pdb=" CG GLU A 330 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 14584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 19533 1.78 - 3.56: 189 3.56 - 5.34: 25 5.34 - 7.12: 8 7.12 - 8.90: 1 Bond angle restraints: 19756 Sorted by residual: angle pdb=" CA GLU A 525 " pdb=" CB GLU A 525 " pdb=" CG GLU A 525 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB GLU A 525 " pdb=" CG GLU A 525 " pdb=" CD GLU A 525 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.70e+00 3.46e-01 1.10e+01 angle pdb=" CB GLU C 330 " pdb=" CG GLU C 330 " pdb=" CD GLU C 330 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.70e+00 3.46e-01 1.10e+01 angle pdb=" CA HIS B 450 " pdb=" C HIS B 450 " pdb=" O HIS B 450 " ideal model delta sigma weight residual 120.10 116.63 3.47 1.13e+00 7.83e-01 9.46e+00 angle pdb=" CB GLU A 330 " pdb=" CG GLU A 330 " pdb=" CD GLU A 330 " ideal model delta sigma weight residual 112.60 117.78 -5.18 1.70e+00 3.46e-01 9.28e+00 ... (remaining 19751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7766 17.79 - 35.59: 886 35.59 - 53.38: 247 53.38 - 71.18: 58 71.18 - 88.97: 27 Dihedral angle restraints: 8984 sinusoidal: 3586 harmonic: 5398 Sorted by residual: dihedral pdb=" CA ASN A 115 " pdb=" C ASN A 115 " pdb=" N TYR A 116 " pdb=" CA TYR A 116 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP C 420 " pdb=" C ASP C 420 " pdb=" N LYS C 421 " pdb=" CA LYS C 421 " ideal model delta harmonic sigma weight residual 180.00 158.45 21.55 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR C 114 " pdb=" C THR C 114 " pdb=" N ASN C 115 " pdb=" CA ASN C 115 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 8981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1342 0.028 - 0.056: 580 0.056 - 0.084: 188 0.084 - 0.112: 166 0.112 - 0.140: 37 Chirality restraints: 2313 Sorted by residual: chirality pdb=" CA ILE C 437 " pdb=" N ILE C 437 " pdb=" C ILE C 437 " pdb=" CB ILE C 437 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CG LEU C 117 " pdb=" CB LEU C 117 " pdb=" CD1 LEU C 117 " pdb=" CD2 LEU C 117 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ASP A 375 " pdb=" N ASP A 375 " pdb=" C ASP A 375 " pdb=" CB ASP A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 2310 not shown) Planarity restraints: 2558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 330 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" CD GLU A 330 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 330 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 330 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 332 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO C 333 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 221 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO C 222 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 222 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 222 " 0.022 5.00e-02 4.00e+02 ... (remaining 2555 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 6415 2.96 - 3.44: 14462 3.44 - 3.93: 24283 3.93 - 4.41: 28399 4.41 - 4.90: 46007 Nonbonded interactions: 119566 Sorted by model distance: nonbonded pdb=" N GLU A 525 " pdb=" OE1 GLU A 525 " model vdw 2.472 3.120 nonbonded pdb=" N GLU C 330 " pdb=" OE1 GLU C 330 " model vdw 2.492 3.120 nonbonded pdb=" N GLU A 330 " pdb=" OE1 GLU A 330 " model vdw 2.510 3.120 nonbonded pdb=" N GLU C 608 " pdb=" OE1 GLU C 608 " model vdw 2.563 3.120 nonbonded pdb=" C THR C 646 " pdb=" OG1 THR C 646 " model vdw 2.578 2.616 ... (remaining 119561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 440 or resid 443 through 668 or resid 901)) selection = (chain 'B' and (resid 46 through 440 or resid 443 through 901)) selection = (chain 'C' and (resid 46 through 668 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.390 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 : 0.003 0.042 14589 Z= 0.130 Angle : 0.471 8.898 19756 Z= 0.249 Chirality : 0.043 0.140 2313 Planarity : 0.004 0.049 2558 Dihedral : 17.130 88.974 5502 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.70 % Allowed : 23.43 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1861 helix: 0.64 (0.18), residues: 722 sheet: 1.50 (0.26), residues: 436 loop : 0.06 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 103 TYR 0.013 0.001 TYR A 334 PHE 0.015 0.001 PHE A 545 TRP 0.006 0.001 TRP A 184 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00293 (14589) covalent geometry : angle 0.47087 (19756) hydrogen bonds : bond 0.21237 ( 834) hydrogen bonds : angle 7.89933 ( 2400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.637 Fit side-chains REVERT: C 119 ARG cc_start: 0.5882 (mmm160) cc_final: 0.5292 (mmp-170) REVERT: C 121 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6817 (pp) REVERT: C 206 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7559 (ttp-110) REVERT: C 319 ASP cc_start: 0.8378 (t0) cc_final: 0.8019 (t0) REVERT: C 516 LYS cc_start: 0.8683 (tppp) cc_final: 0.8122 (tppt) REVERT: A 419 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6240 (mmmt) REVERT: A 428 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8274 (mp0) REVERT: A 516 LYS cc_start: 0.8840 (ttpp) cc_final: 0.8594 (ttmt) REVERT: A 616 LYS cc_start: 0.8207 (tttt) cc_final: 0.7925 (tttt) REVERT: B 55 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8545 (tppp) REVERT: B 126 LYS cc_start: 0.7866 (ttmt) cc_final: 0.7494 (tptp) REVERT: B 206 ARG cc_start: 0.8633 (ttp80) cc_final: 0.8421 (ttt-90) REVERT: B 346 GLU cc_start: 0.7886 (tt0) cc_final: 0.7298 (tm-30) REVERT: B 366 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8528 (m) REVERT: B 653 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8418 (p) outliers start: 27 outliers final: 18 residues processed: 140 average time/residue: 0.7160 time to fit residues: 109.0800 Evaluate side-chains 141 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 632 GLN A 369 ASN B 450 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.085388 restraints weight = 22603.032| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.22 r_work: 0.2930 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14589 Z= 0.210 Angle : 0.542 6.161 19756 Z= 0.298 Chirality : 0.046 0.152 2313 Planarity : 0.004 0.046 2558 Dihedral : 6.213 95.225 2046 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.60 % Allowed : 20.03 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1861 helix: 1.75 (0.18), residues: 728 sheet: 1.49 (0.25), residues: 436 loop : -0.07 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 103 TYR 0.019 0.002 TYR A 334 PHE 0.021 0.002 PHE A 663 TRP 0.004 0.001 TRP B 184 HIS 0.005 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00473 (14589) covalent geometry : angle 0.54230 (19756) hydrogen bonds : bond 0.06336 ( 834) hydrogen bonds : angle 5.53930 ( 2400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 123 time to evaluate : 0.611 Fit side-chains REVERT: C 119 ARG cc_start: 0.6116 (mmm160) cc_final: 0.5422 (mmp-170) REVERT: C 206 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7329 (mtp-110) REVERT: C 261 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: C 378 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8036 (ttpm) REVERT: C 516 LYS cc_start: 0.8697 (tppp) cc_final: 0.8096 (tppt) REVERT: C 611 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8729 (mp10) REVERT: A 57 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: A 96 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8112 (ttm) REVERT: A 112 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7266 (mp) REVERT: A 419 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6246 (mmmt) REVERT: A 428 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8333 (mp0) REVERT: A 516 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8547 (ttmt) REVERT: A 616 LYS cc_start: 0.8239 (tttt) cc_final: 0.7960 (tttt) REVERT: B 55 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8619 (tppp) REVERT: B 126 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7369 (mmtt) REVERT: B 206 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8353 (ttt-90) REVERT: B 325 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7870 (mmmt) REVERT: B 346 GLU cc_start: 0.7710 (tt0) cc_final: 0.7156 (tm-30) REVERT: B 653 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8332 (p) outliers start: 73 outliers final: 33 residues processed: 185 average time/residue: 0.6634 time to fit residues: 133.5830 Evaluate side-chains 163 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 22 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 587 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086217 restraints weight = 22827.893| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.24 r_work: 0.2944 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14589 Z= 0.166 Angle : 0.504 6.254 19756 Z= 0.275 Chirality : 0.045 0.146 2313 Planarity : 0.004 0.043 2558 Dihedral : 5.363 59.867 2031 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.09 % Allowed : 20.40 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.20), residues: 1861 helix: 1.95 (0.18), residues: 733 sheet: 1.43 (0.25), residues: 438 loop : -0.06 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 103 TYR 0.020 0.002 TYR A 334 PHE 0.017 0.001 PHE A 663 TRP 0.005 0.001 TRP B 184 HIS 0.003 0.000 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00365 (14589) covalent geometry : angle 0.50449 (19756) hydrogen bonds : bond 0.05578 ( 834) hydrogen bonds : angle 5.20993 ( 2400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 126 time to evaluate : 0.663 Fit side-chains REVERT: C 119 ARG cc_start: 0.6161 (mmm160) cc_final: 0.5551 (mmp-170) REVERT: C 207 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8340 (mptp) REVERT: C 516 LYS cc_start: 0.8699 (tppp) cc_final: 0.8102 (tppt) REVERT: C 611 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8734 (mp10) REVERT: C 667 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7454 (mt) REVERT: A 57 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: A 96 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8071 (ttm) REVERT: A 112 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7225 (mp) REVERT: A 199 GLU cc_start: 0.8373 (pm20) cc_final: 0.8149 (pm20) REVERT: A 419 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6205 (mmmt) REVERT: A 428 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8273 (mp0) REVERT: A 516 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8536 (ttmt) REVERT: A 616 LYS cc_start: 0.8237 (tttt) cc_final: 0.7976 (tttt) REVERT: A 645 GLU cc_start: 0.6751 (pm20) cc_final: 0.6530 (pm20) REVERT: B 54 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8146 (mmt90) REVERT: B 55 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8616 (tppp) REVERT: B 119 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7240 (mmt180) REVERT: B 126 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7350 (mmtt) REVERT: B 206 ARG cc_start: 0.8585 (ttp80) cc_final: 0.8375 (ttt-90) REVERT: B 230 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: B 325 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7820 (mmmt) REVERT: B 346 GLU cc_start: 0.7714 (tt0) cc_final: 0.7145 (tm-30) REVERT: B 583 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8636 (mptp) REVERT: B 587 GLN cc_start: 0.8579 (tt0) cc_final: 0.8322 (tm-30) REVERT: B 661 ARG cc_start: 0.7403 (mpp80) cc_final: 0.6687 (mpp80) outliers start: 65 outliers final: 26 residues processed: 183 average time/residue: 0.7556 time to fit residues: 149.6587 Evaluate side-chains 159 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 369 ASN A 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.103550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.084953 restraints weight = 22777.658| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.22 r_work: 0.2917 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14589 Z= 0.227 Angle : 0.540 5.771 19756 Z= 0.294 Chirality : 0.046 0.156 2313 Planarity : 0.004 0.044 2558 Dihedral : 5.385 55.951 2025 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.47 % Allowed : 19.65 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1861 helix: 1.93 (0.18), residues: 734 sheet: 1.39 (0.25), residues: 438 loop : -0.14 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 103 TYR 0.022 0.002 TYR A 334 PHE 0.019 0.001 PHE A 545 TRP 0.004 0.001 TRP B 184 HIS 0.009 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00520 (14589) covalent geometry : angle 0.54000 (19756) hydrogen bonds : bond 0.05726 ( 834) hydrogen bonds : angle 5.20634 ( 2400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 0.639 Fit side-chains REVERT: C 119 ARG cc_start: 0.6170 (mmm160) cc_final: 0.5429 (mmp-170) REVERT: C 207 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8333 (mptp) REVERT: C 230 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: C 516 LYS cc_start: 0.8741 (tppp) cc_final: 0.8140 (tppt) REVERT: C 611 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8763 (mp10) REVERT: C 667 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7435 (mt) REVERT: A 57 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: A 96 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8109 (ttm) REVERT: A 112 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7145 (mp) REVERT: A 199 GLU cc_start: 0.8376 (pm20) cc_final: 0.8116 (pm20) REVERT: A 315 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8376 (tmmm) REVERT: A 409 ASP cc_start: 0.1454 (OUTLIER) cc_final: 0.1127 (p0) REVERT: A 428 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8324 (mp0) REVERT: A 516 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8548 (ttmt) REVERT: A 616 LYS cc_start: 0.8279 (tttt) cc_final: 0.8060 (tttt) REVERT: A 645 GLU cc_start: 0.6752 (pm20) cc_final: 0.6534 (pm20) REVERT: B 54 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7537 (mmt90) REVERT: B 119 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7282 (mmt180) REVERT: B 126 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7358 (mmtt) REVERT: B 230 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: B 325 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7805 (mmmt) REVERT: B 346 GLU cc_start: 0.7731 (tt0) cc_final: 0.7168 (tm-30) REVERT: B 456 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7808 (mtmt) REVERT: B 587 GLN cc_start: 0.8597 (tt0) cc_final: 0.8340 (tm-30) outliers start: 71 outliers final: 42 residues processed: 191 average time/residue: 0.6962 time to fit residues: 144.5154 Evaluate side-chains 181 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 34 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087605 restraints weight = 22604.832| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.24 r_work: 0.2966 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14589 Z= 0.127 Angle : 0.480 6.440 19756 Z= 0.262 Chirality : 0.044 0.143 2313 Planarity : 0.004 0.043 2558 Dihedral : 4.818 55.615 2015 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.03 % Allowed : 20.59 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.20), residues: 1861 helix: 2.18 (0.18), residues: 737 sheet: 1.33 (0.25), residues: 438 loop : -0.07 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 103 TYR 0.022 0.001 TYR A 334 PHE 0.025 0.001 PHE A 663 TRP 0.007 0.001 TRP A 184 HIS 0.009 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00270 (14589) covalent geometry : angle 0.48050 (19756) hydrogen bonds : bond 0.04770 ( 834) hydrogen bonds : angle 4.90475 ( 2400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 0.686 Fit side-chains REVERT: C 119 ARG cc_start: 0.6176 (mmm160) cc_final: 0.5520 (mmp-170) REVERT: C 207 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8492 (mmmt) REVERT: C 230 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: C 516 LYS cc_start: 0.8699 (tppp) cc_final: 0.8107 (tppt) REVERT: C 611 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8729 (mp10) REVERT: C 667 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7451 (mt) REVERT: A 87 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8417 (mmpt) REVERT: A 96 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7949 (ttm) REVERT: A 285 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8126 (ptmm) REVERT: A 315 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8347 (tmmm) REVERT: A 428 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8498 (mt-10) REVERT: A 516 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8569 (ttmt) REVERT: B 54 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8182 (mmt90) REVERT: B 119 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7221 (mmt180) REVERT: B 126 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7339 (mmtt) REVERT: B 230 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: B 325 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7743 (mmmt) REVERT: B 346 GLU cc_start: 0.7704 (tt0) cc_final: 0.7156 (tm-30) REVERT: B 456 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7798 (mtmt) REVERT: B 587 GLN cc_start: 0.8590 (tt0) cc_final: 0.8334 (tm-30) outliers start: 64 outliers final: 24 residues processed: 183 average time/residue: 0.7260 time to fit residues: 144.1326 Evaluate side-chains 156 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 99 optimal weight: 0.0270 chunk 45 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 369 ASN A 658 HIS B 450 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.103393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.084761 restraints weight = 22779.496| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.22 r_work: 0.2914 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14589 Z= 0.250 Angle : 0.564 10.815 19756 Z= 0.303 Chirality : 0.047 0.167 2313 Planarity : 0.004 0.044 2558 Dihedral : 5.042 57.421 2012 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.97 % Allowed : 20.97 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1861 helix: 2.00 (0.18), residues: 732 sheet: 1.30 (0.25), residues: 441 loop : -0.16 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 103 TYR 0.022 0.002 TYR A 334 PHE 0.027 0.002 PHE C 663 TRP 0.003 0.001 TRP B 184 HIS 0.009 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00577 (14589) covalent geometry : angle 0.56401 (19756) hydrogen bonds : bond 0.05659 ( 834) hydrogen bonds : angle 5.13151 ( 2400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 0.604 Fit side-chains REVERT: C 56 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7985 (tp) REVERT: C 207 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8347 (mptp) REVERT: C 230 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7907 (tm-30) REVERT: C 516 LYS cc_start: 0.8753 (tppp) cc_final: 0.8153 (tppt) REVERT: C 611 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8743 (mp10) REVERT: C 667 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7467 (mt) REVERT: A 96 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8106 (ttm) REVERT: A 285 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8163 (ptmm) REVERT: A 315 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8397 (tmmm) REVERT: A 428 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8549 (mt-10) REVERT: A 516 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8588 (ttmt) REVERT: A 616 LYS cc_start: 0.8262 (tttm) cc_final: 0.7981 (tttt) REVERT: A 645 GLU cc_start: 0.6753 (pm20) cc_final: 0.6528 (pm20) REVERT: B 54 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7666 (mmt90) REVERT: B 119 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7285 (mmt180) REVERT: B 126 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7368 (mmtt) REVERT: B 230 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7790 (tp30) REVERT: B 325 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7738 (mmmt) REVERT: B 346 GLU cc_start: 0.7731 (tt0) cc_final: 0.7167 (tm-30) REVERT: B 456 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7805 (mtmt) REVERT: B 587 GLN cc_start: 0.8614 (tt0) cc_final: 0.8335 (tm-30) outliers start: 63 outliers final: 31 residues processed: 177 average time/residue: 0.6030 time to fit residues: 116.1730 Evaluate side-chains 165 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 54 ARG Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 544 ASP Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087656 restraints weight = 22539.358| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.23 r_work: 0.2966 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14589 Z= 0.128 Angle : 0.496 6.291 19756 Z= 0.268 Chirality : 0.044 0.141 2313 Planarity : 0.004 0.044 2558 Dihedral : 4.755 57.577 2012 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.34 % Allowed : 21.35 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1861 helix: 2.23 (0.19), residues: 731 sheet: 1.27 (0.25), residues: 439 loop : -0.11 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 103 TYR 0.023 0.001 TYR A 334 PHE 0.016 0.001 PHE A 663 TRP 0.008 0.001 TRP A 184 HIS 0.008 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00275 (14589) covalent geometry : angle 0.49626 (19756) hydrogen bonds : bond 0.04702 ( 834) hydrogen bonds : angle 4.86120 ( 2400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 0.462 Fit side-chains REVERT: C 56 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7988 (tp) REVERT: C 207 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8525 (mmmt) REVERT: C 516 LYS cc_start: 0.8681 (tppp) cc_final: 0.8080 (tppt) REVERT: C 611 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8724 (mp10) REVERT: C 667 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7465 (mt) REVERT: A 87 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8415 (mmpt) REVERT: A 96 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7927 (ttm) REVERT: A 112 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7205 (mp) REVERT: A 285 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8115 (ptmm) REVERT: A 315 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8358 (tmmm) REVERT: A 428 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8503 (mt-10) REVERT: A 516 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8558 (ttmt) REVERT: A 645 GLU cc_start: 0.6704 (pm20) cc_final: 0.6485 (pm20) REVERT: B 119 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7208 (mmt180) REVERT: B 126 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7348 (mmtt) REVERT: B 230 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: B 325 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7684 (mmmt) REVERT: B 346 GLU cc_start: 0.7687 (tt0) cc_final: 0.7141 (tm-30) REVERT: B 456 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7825 (mtpt) REVERT: B 587 GLN cc_start: 0.8573 (tt0) cc_final: 0.8331 (tm-30) outliers start: 53 outliers final: 22 residues processed: 178 average time/residue: 0.7530 time to fit residues: 144.7196 Evaluate side-chains 159 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 611 GLN Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 82 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 658 HIS B 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087331 restraints weight = 22583.098| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.23 r_work: 0.2960 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14589 Z= 0.147 Angle : 0.510 6.381 19756 Z= 0.274 Chirality : 0.044 0.149 2313 Planarity : 0.004 0.044 2558 Dihedral : 4.733 57.731 2011 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.40 % Allowed : 21.85 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.20), residues: 1861 helix: 2.24 (0.18), residues: 732 sheet: 1.29 (0.25), residues: 442 loop : -0.09 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 103 TYR 0.024 0.002 TYR A 334 PHE 0.031 0.001 PHE C 663 TRP 0.006 0.001 TRP B 184 HIS 0.008 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00327 (14589) covalent geometry : angle 0.50963 (19756) hydrogen bonds : bond 0.04756 ( 834) hydrogen bonds : angle 4.85416 ( 2400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 127 time to evaluate : 0.596 Fit side-chains REVERT: C 56 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7934 (tp) REVERT: C 207 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8546 (mmmt) REVERT: C 230 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: C 516 LYS cc_start: 0.8692 (tppp) cc_final: 0.8091 (tppt) REVERT: C 667 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7458 (mt) REVERT: A 87 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8409 (mmpt) REVERT: A 96 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7942 (ttm) REVERT: A 112 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7223 (mp) REVERT: A 285 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8119 (ptmm) REVERT: A 315 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8373 (tmmm) REVERT: A 428 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8519 (mt-10) REVERT: A 516 LYS cc_start: 0.8849 (ttpp) cc_final: 0.8580 (ttmt) REVERT: A 616 LYS cc_start: 0.8090 (tttt) cc_final: 0.7779 (tttt) REVERT: A 645 GLU cc_start: 0.6729 (pm20) cc_final: 0.6504 (pm20) REVERT: B 119 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7210 (mmt180) REVERT: B 126 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7347 (mmtt) REVERT: B 230 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7813 (tp30) REVERT: B 325 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7683 (mmmt) REVERT: B 346 GLU cc_start: 0.7694 (tt0) cc_final: 0.7147 (tm-30) REVERT: B 456 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7821 (mtmt) REVERT: B 587 GLN cc_start: 0.8622 (tt0) cc_final: 0.8368 (tm-30) outliers start: 54 outliers final: 30 residues processed: 174 average time/residue: 0.6823 time to fit residues: 128.7708 Evaluate side-chains 169 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 161 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 658 HIS B 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.105671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.087021 restraints weight = 22650.756| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.23 r_work: 0.2954 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14589 Z= 0.160 Angle : 0.523 6.300 19756 Z= 0.281 Chirality : 0.045 0.177 2313 Planarity : 0.004 0.043 2558 Dihedral : 4.769 58.697 2011 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.21 % Allowed : 22.10 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.20), residues: 1861 helix: 2.20 (0.19), residues: 734 sheet: 1.28 (0.25), residues: 442 loop : -0.10 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 103 TYR 0.026 0.002 TYR A 334 PHE 0.018 0.001 PHE A 663 TRP 0.005 0.001 TRP B 184 HIS 0.008 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00361 (14589) covalent geometry : angle 0.52288 (19756) hydrogen bonds : bond 0.04869 ( 834) hydrogen bonds : angle 4.89061 ( 2400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.538 Fit side-chains REVERT: C 56 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7937 (tp) REVERT: C 207 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8541 (mmmt) REVERT: C 230 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: C 516 LYS cc_start: 0.8703 (tppp) cc_final: 0.8103 (tppt) REVERT: C 667 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7470 (mt) REVERT: A 87 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8414 (mmpt) REVERT: A 96 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7966 (ttm) REVERT: A 112 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7252 (mp) REVERT: A 285 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8119 (ptmm) REVERT: A 315 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8395 (tmmm) REVERT: A 428 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8526 (mt-10) REVERT: A 516 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8584 (ttmt) REVERT: A 616 LYS cc_start: 0.8077 (tttt) cc_final: 0.7664 (tttt) REVERT: A 645 GLU cc_start: 0.6733 (pm20) cc_final: 0.6506 (pm20) REVERT: B 119 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7218 (mmt180) REVERT: B 126 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7357 (mmtt) REVERT: B 230 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: B 325 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7672 (mmmt) REVERT: B 346 GLU cc_start: 0.7726 (tt0) cc_final: 0.7173 (tm-30) REVERT: B 456 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.7827 (mtmt) REVERT: B 587 GLN cc_start: 0.8624 (tt0) cc_final: 0.8367 (tm-30) REVERT: B 653 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8262 (p) outliers start: 51 outliers final: 31 residues processed: 172 average time/residue: 0.6470 time to fit residues: 120.6504 Evaluate side-chains 171 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 591 LYS Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 151 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 658 HIS B 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.084528 restraints weight = 22725.135| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.22 r_work: 0.2913 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14589 Z= 0.260 Angle : 0.599 7.195 19756 Z= 0.322 Chirality : 0.048 0.191 2313 Planarity : 0.005 0.045 2558 Dihedral : 5.138 58.644 2011 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.27 % Allowed : 22.17 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.20), residues: 1861 helix: 1.99 (0.18), residues: 726 sheet: 1.25 (0.25), residues: 444 loop : -0.22 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 103 TYR 0.028 0.002 TYR A 334 PHE 0.038 0.002 PHE C 663 TRP 0.002 0.001 TRP C 184 HIS 0.008 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00602 (14589) covalent geometry : angle 0.59853 (19756) hydrogen bonds : bond 0.05781 ( 834) hydrogen bonds : angle 5.16134 ( 2400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3722 Ramachandran restraints generated. 1861 Oldfield, 0 Emsley, 1861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.601 Fit side-chains REVERT: C 56 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7973 (tp) REVERT: C 207 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8339 (mptp) REVERT: C 230 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: C 516 LYS cc_start: 0.8750 (tppp) cc_final: 0.8141 (tppt) REVERT: C 667 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7398 (mt) REVERT: A 87 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (mmpt) REVERT: A 96 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8155 (ttm) REVERT: A 112 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7212 (mp) REVERT: A 285 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8189 (ptmm) REVERT: A 315 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8398 (tmmm) REVERT: A 428 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8550 (mt-10) REVERT: A 516 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8550 (ttmt) REVERT: A 645 GLU cc_start: 0.6744 (pm20) cc_final: 0.6492 (pm20) REVERT: B 119 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7272 (mmt180) REVERT: B 126 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7353 (mmtt) REVERT: B 230 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: B 325 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7671 (mmmt) REVERT: B 346 GLU cc_start: 0.7740 (tt0) cc_final: 0.7180 (tm-30) REVERT: B 456 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7807 (mtmt) REVERT: B 587 GLN cc_start: 0.8619 (tt0) cc_final: 0.8350 (tm-30) REVERT: B 653 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8301 (p) outliers start: 52 outliers final: 27 residues processed: 167 average time/residue: 0.6506 time to fit residues: 118.0570 Evaluate side-chains 163 residues out of total 1588 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 667 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 158 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 HIS B 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086044 restraints weight = 22743.472| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.23 r_work: 0.2942 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14589 Z= 0.170 Angle : 0.548 7.206 19756 Z= 0.295 Chirality : 0.045 0.183 2313 Planarity : 0.004 0.044 2558 Dihedral : 4.989 58.118 2011 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.02 % Allowed : 22.36 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1861 helix: 2.08 (0.19), residues: 732 sheet: 1.23 (0.25), residues: 441 loop : -0.18 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 103 TYR 0.027 0.002 TYR A 334 PHE 0.021 0.001 PHE A 663 TRP 0.004 0.001 TRP C 184 HIS 0.008 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00381 (14589) covalent geometry : angle 0.54850 (19756) hydrogen bonds : bond 0.05201 ( 834) hydrogen bonds : angle 5.02314 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.37 seconds wall clock time: 81 minutes 18.24 seconds (4878.24 seconds total)