Starting phenix.real_space_refine on Sun Aug 24 03:13:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjr_62372/08_2025/9kjr_62372.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjr_62372/08_2025/9kjr_62372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kjr_62372/08_2025/9kjr_62372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjr_62372/08_2025/9kjr_62372.map" model { file = "/net/cci-nas-00/data/ceres_data/9kjr_62372/08_2025/9kjr_62372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjr_62372/08_2025/9kjr_62372.cif" } resolution = 3.86 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= 0.002 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10359 2.51 5 N 2820 2.21 5 O 3162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16413 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5471 Classifications: {'peptide': 710} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675} Chain: "B" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5471 Classifications: {'peptide': 710} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675} Chain: "C" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5471 Classifications: {'peptide': 710} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 675} Time building chain proxies: 3.38, per 1000 atoms: 0.21 Number of scatterers: 16413 At special positions: 0 Unit cell: (108.73, 106.24, 122.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3162 8.00 N 2820 7.00 C 10359 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: 1.39 Conformation dependent library (CDL) restraints added in 530.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 17 sheets defined 39.3% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... 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 165 through 180 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 238 through 267 Processing helix chain 'A' and resid 280 through 301 removed outlier: 5.614A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 removed outlier: 3.651A pdb=" N ARG A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.670A pdb=" N ILE A 336 " --> pdb=" O ASP A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 409 through 417 removed outlier: 3.707A pdb=" N THR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN A 416 " --> pdb=" O ILE A 412 " (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 499 removed outlier: 3.518A pdb=" N GLY A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 541 Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.792A pdb=" N VAL A 571 " --> pdb=" O PRO A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 636 removed outlier: 3.792A pdb=" N THR A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 719 through 724 removed outlier: 3.506A pdb=" N ALA A 722 " --> pdb=" O HIS A 719 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY A 724 " --> pdb=" O THR A 721 " (cutoff:3.500A) 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 165 through 179 removed outlier: 3.536A pdb=" N ASN B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 removed outlier: 3.589A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.510A pdb=" N PHE B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 removed outlier: 6.003A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 Processing helix chain 'B' and resid 332 through 356 Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 409 through 417 removed outlier: 3.531A pdb=" N THR B 413 " --> pdb=" O ASP B 409 " (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 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 534 through 541 Processing helix chain 'B' and resid 567 through 591 removed outlier: 3.789A pdb=" N VAL B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 4.088A pdb=" N ALA B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 653 through 669 Processing helix chain 'B' and resid 708 through 712 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.831A pdb=" N ALA C 108 " --> pdb=" O LYS C 105 " (cutoff:3.500A) 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 165 through 180 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.759A pdb=" N PHE C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE C 255 " --> pdb=" O TYR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 5.881A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.586A pdb=" N ASP C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 Processing helix chain 'C' and resid 401 through 406 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 498 Processing helix chain 'C' and resid 534 through 541 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.749A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 593 " --> pdb=" O MET C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 4.372A pdb=" N LYS C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 636 removed outlier: 3.780A pdb=" N GLU C 634 " --> pdb=" O LYS C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 668 Processing helix chain 'C' and resid 719 through 724 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51 removed outlier: 6.490A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 3.615A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP A 526 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.280A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET A 424 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N SER A 474 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N HIS A 426 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 476 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLU A 428 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N GLU A 478 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'A' and resid 681 through 686 removed outlier: 4.072A pdb=" N VAL A 705 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU A 706 " --> pdb=" O MET A 745 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 747 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 737 " --> pdb=" O ARG A 746 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N SER A 748 " --> pdb=" O TYR A 735 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR A 735 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.618A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 156 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 202 removed outlier: 3.550A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN B 235 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLY B 553 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR B 550 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.487A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N MET B 424 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER B 474 " --> pdb=" O MET B 424 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS B 426 " --> pdb=" O SER B 474 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 476 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLU B 428 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLU B 478 " --> pdb=" O GLU B 428 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 611 Processing sheet with id=AB1, first strand: chain 'B' and resid 705 through 707 Processing sheet with id=AB2, first strand: chain 'B' and resid 738 through 739 Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 51 removed outlier: 6.479A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP C 149 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 202 removed outlier: 3.855A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA C 231 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL C 217 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU C 229 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 219 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 370 through 374 removed outlier: 6.399A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET C 424 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N SER C 474 " --> pdb=" O MET C 424 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS C 426 " --> pdb=" O SER C 474 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL C 476 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU C 428 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N GLU C 478 " --> pdb=" O GLU C 428 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 606 through 611 Processing sheet with id=AB7, first strand: chain 'C' and resid 682 through 685 removed outlier: 5.433A pdb=" N TYR C 735 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER C 748 " --> pdb=" O TYR C 735 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY C 737 " --> pdb=" O ARG C 746 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 695 through 696 888 hydrogen bonds defined for protein. 2454 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: 2.51 Time building geometry restraints manager: 1.77 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: 5494 1.34 - 1.46: 3338 1.46 - 1.58: 7722 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 16677 Sorted by residual: bond pdb=" CA SER B 498 " pdb=" C SER B 498 " ideal model delta sigma weight residual 1.522 1.486 0.035 1.72e-02 3.38e+03 4.24e+00 bond pdb=" C GLY B 52 " pdb=" N ASN B 53 " ideal model delta sigma weight residual 1.332 1.317 0.016 1.40e-02 5.10e+03 1.27e+00 bond pdb=" CB MET A 589 " pdb=" CG MET A 589 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.95e-01 bond pdb=" C LYS C 562 " pdb=" N LEU C 563 " ideal model delta sigma weight residual 1.339 1.285 0.054 5.57e-02 3.22e+02 9.56e-01 bond pdb=" CB TRP C 184 " pdb=" CG TRP C 184 " ideal model delta sigma weight residual 1.498 1.468 0.030 3.10e-02 1.04e+03 9.49e-01 ... (remaining 16672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 22315 2.43 - 4.86: 225 4.86 - 7.29: 22 7.29 - 9.72: 6 9.72 - 12.15: 4 Bond angle restraints: 22572 Sorted by residual: angle pdb=" CB MET C 44 " pdb=" CG MET C 44 " pdb=" SD MET C 44 " ideal model delta sigma weight residual 112.70 124.85 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CB MET C 702 " pdb=" CG MET C 702 " pdb=" SD MET C 702 " ideal model delta sigma weight residual 112.70 123.83 -11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CB MET B 228 " pdb=" CG MET B 228 " pdb=" SD MET B 228 " ideal model delta sigma weight residual 112.70 123.82 -11.12 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CB MET C 292 " pdb=" CG MET C 292 " pdb=" SD MET C 292 " ideal model delta sigma weight residual 112.70 122.60 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB MET B 292 " pdb=" CG MET B 292 " pdb=" SD MET B 292 " ideal model delta sigma weight residual 112.70 121.97 -9.27 3.00e+00 1.11e-01 9.55e+00 ... (remaining 22567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 8809 17.74 - 35.47: 1064 35.47 - 53.20: 293 53.20 - 70.94: 67 70.94 - 88.67: 45 Dihedral angle restraints: 10278 sinusoidal: 4131 harmonic: 6147 Sorted by residual: dihedral pdb=" CA PRO C 613 " pdb=" C PRO C 613 " pdb=" N LEU C 614 " pdb=" CA LEU C 614 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA VAL B 121 " pdb=" C VAL B 121 " pdb=" N GLY B 122 " pdb=" CA GLY B 122 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLN C 104 " pdb=" C GLN C 104 " pdb=" N LYS C 105 " pdb=" CA LYS C 105 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 10275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1602 0.028 - 0.057: 579 0.057 - 0.085: 252 0.085 - 0.113: 163 0.113 - 0.142: 38 Chirality restraints: 2634 Sorted by residual: chirality pdb=" CA VAL C 610 " pdb=" N VAL C 610 " pdb=" C VAL C 610 " pdb=" CB VAL C 610 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE B 689 " pdb=" N ILE B 689 " pdb=" C ILE B 689 " pdb=" CB ILE B 689 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE A 462 " pdb=" N ILE A 462 " pdb=" C ILE A 462 " pdb=" CB ILE A 462 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 2631 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 595 " -0.034 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO C 596 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 596 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 596 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET B 745 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C MET B 745 " 0.031 2.00e-02 2.50e+03 pdb=" O MET B 745 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG B 746 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 699 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 700 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 700 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 700 " 0.021 5.00e-02 4.00e+02 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2745 2.76 - 3.29: 17577 3.29 - 3.83: 28970 3.83 - 4.36: 31360 4.36 - 4.90: 54048 Nonbonded interactions: 134700 Sorted by model distance: nonbonded pdb=" OG SER C 615 " pdb=" O PRO C 740 " model vdw 2.219 3.040 nonbonded pdb=" O GLN A 576 " pdb=" OG SER A 579 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR A 427 " pdb=" OG SER A 483 " model vdw 2.233 3.040 nonbonded pdb=" O THR B 550 " pdb=" NZ LYS B 582 " model vdw 2.242 3.120 nonbonded pdb=" OG1 THR B 515 " pdb=" OD2 ASP B 542 " model vdw 2.248 3.040 ... (remaining 134695 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.250 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16677 Z= 0.223 Angle : 0.627 12.152 22572 Z= 0.315 Chirality : 0.042 0.142 2634 Planarity : 0.004 0.053 2931 Dihedral : 17.735 88.674 6318 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.28 % Allowed : 30.30 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.19), residues: 2124 helix: 2.46 (0.19), residues: 716 sheet: 0.46 (0.24), residues: 499 loop : -0.94 (0.22), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 749 TYR 0.016 0.001 TYR B 334 PHE 0.010 0.001 PHE B 736 TRP 0.007 0.002 TRP B 184 HIS 0.005 0.001 HIS B 708 Details of bonding type rmsd covalent geometry : bond 0.00474 (16677) covalent geometry : angle 0.62692 (22572) hydrogen bonds : bond 0.13266 ( 888) hydrogen bonds : angle 6.16794 ( 2454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 209 MET cc_start: 0.9154 (mpp) cc_final: 0.8833 (mpp) outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 0.1119 time to fit residues: 11.9667 Evaluate side-chains 61 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 653 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0470 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN ** B 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 392 GLN C 632 GLN C 675 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.063951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.042900 restraints weight = 86739.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.044226 restraints weight = 52136.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.045162 restraints weight = 37467.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.045727 restraints weight = 30034.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.046211 restraints weight = 26117.161| |-----------------------------------------------------------------------------| r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16677 Z= 0.172 Angle : 0.554 6.981 22572 Z= 0.288 Chirality : 0.043 0.141 2634 Planarity : 0.004 0.058 2931 Dihedral : 4.149 26.382 2294 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.81 % Allowed : 27.92 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 2124 helix: 2.53 (0.19), residues: 732 sheet: 0.46 (0.23), residues: 502 loop : -0.90 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 749 TYR 0.017 0.001 TYR B 334 PHE 0.012 0.001 PHE A 545 TRP 0.004 0.001 TRP B 184 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00371 (16677) covalent geometry : angle 0.55401 (22572) hydrogen bonds : bond 0.04349 ( 888) hydrogen bonds : angle 5.03545 ( 2454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 61 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.5991 (t80) REVERT: C 184 TRP cc_start: 0.9162 (OUTLIER) cc_final: 0.8710 (t60) REVERT: C 209 MET cc_start: 0.9186 (mpp) cc_final: 0.8789 (mpp) REVERT: C 424 MET cc_start: 0.8339 (tmm) cc_final: 0.8086 (tmm) REVERT: C 496 MET cc_start: 0.9258 (mmm) cc_final: 0.9053 (tpp) REVERT: C 577 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.8981 (mt0) REVERT: C 675 GLN cc_start: 0.4911 (OUTLIER) cc_final: 0.4520 (mm110) REVERT: C 695 MET cc_start: 0.1763 (tpt) cc_final: 0.1530 (tpp) outliers start: 51 outliers final: 28 residues processed: 107 average time/residue: 0.1213 time to fit residues: 21.2438 Evaluate side-chains 90 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 738 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 675 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 129 optimal weight: 0.0270 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS C 632 GLN C 675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.038862 restraints weight = 82782.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.040126 restraints weight = 52617.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.040892 restraints weight = 39464.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.041599 restraints weight = 33410.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.041831 restraints weight = 29882.078| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16677 Z= 0.123 Angle : 0.527 7.269 22572 Z= 0.272 Chirality : 0.043 0.243 2634 Planarity : 0.004 0.060 2931 Dihedral : 4.086 29.886 2293 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.04 % Allowed : 28.09 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 2124 helix: 2.54 (0.19), residues: 738 sheet: 0.49 (0.23), residues: 503 loop : -0.88 (0.23), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 749 TYR 0.015 0.001 TYR B 334 PHE 0.014 0.001 PHE A 545 TRP 0.002 0.001 TRP B 184 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00266 (16677) covalent geometry : angle 0.52663 (22572) hydrogen bonds : bond 0.03870 ( 888) hydrogen bonds : angle 4.73182 ( 2454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 60 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8460 (tmm) cc_final: 0.8235 (tmm) REVERT: A 228 MET cc_start: 0.8781 (tmm) cc_final: 0.8360 (tmm) REVERT: A 543 MET cc_start: 0.8561 (ppp) cc_final: 0.7743 (ppp) REVERT: B 116 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6033 (t80) REVERT: B 439 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8613 (ttpp) REVERT: C 179 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9328 (tt) REVERT: C 209 MET cc_start: 0.9149 (tpp) cc_final: 0.8647 (mpp) REVERT: C 424 MET cc_start: 0.8371 (tmm) cc_final: 0.8006 (tmm) outliers start: 55 outliers final: 30 residues processed: 109 average time/residue: 0.1310 time to fit residues: 22.7310 Evaluate side-chains 91 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 653 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 81 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 38 optimal weight: 0.0020 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.063946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.038309 restraints weight = 82825.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.039613 restraints weight = 52729.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.040383 restraints weight = 39964.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.041064 restraints weight = 33961.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.041282 restraints weight = 30362.678| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16677 Z= 0.191 Angle : 0.554 7.839 22572 Z= 0.282 Chirality : 0.043 0.175 2634 Planarity : 0.004 0.068 2931 Dihedral : 4.045 22.516 2293 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.48 % Allowed : 28.20 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 2124 helix: 2.54 (0.19), residues: 739 sheet: 0.46 (0.23), residues: 504 loop : -0.93 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 119 TYR 0.015 0.001 TYR B 334 PHE 0.012 0.001 PHE A 545 TRP 0.003 0.001 TRP B 184 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00416 (16677) covalent geometry : angle 0.55428 (22572) hydrogen bonds : bond 0.03879 ( 888) hydrogen bonds : angle 4.70625 ( 2454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 58 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8759 (tmm) cc_final: 0.8383 (tmm) REVERT: A 543 MET cc_start: 0.8640 (ppp) cc_final: 0.7779 (ppp) REVERT: B 116 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6289 (t80) REVERT: B 426 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7733 (t-170) REVERT: B 439 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8650 (ttpp) REVERT: C 179 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9323 (tt) REVERT: C 184 TRP cc_start: 0.9178 (OUTLIER) cc_final: 0.8681 (t60) REVERT: C 424 MET cc_start: 0.8430 (tmm) cc_final: 0.8023 (tmm) REVERT: C 577 GLN cc_start: 0.9516 (OUTLIER) cc_final: 0.9033 (mt0) outliers start: 63 outliers final: 46 residues processed: 116 average time/residue: 0.1177 time to fit residues: 22.6629 Evaluate side-chains 110 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 58 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 653 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 105 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 196 optimal weight: 0.0870 chunk 38 optimal weight: 0.3980 chunk 183 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 HIS ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.042786 restraints weight = 87753.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.044126 restraints weight = 52712.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.045022 restraints weight = 37759.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.045708 restraints weight = 30239.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.046160 restraints weight = 26068.439| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16677 Z= 0.182 Angle : 0.553 8.005 22572 Z= 0.280 Chirality : 0.043 0.144 2634 Planarity : 0.004 0.063 2931 Dihedral : 4.056 22.814 2293 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.97 % Allowed : 27.76 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 2124 helix: 2.54 (0.19), residues: 739 sheet: 0.45 (0.23), residues: 504 loop : -0.94 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 119 TYR 0.015 0.001 TYR B 334 PHE 0.012 0.001 PHE A 545 TRP 0.004 0.001 TRP B 184 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00395 (16677) covalent geometry : angle 0.55290 (22572) hydrogen bonds : bond 0.03857 ( 888) hydrogen bonds : angle 4.66085 ( 2454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 59 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8726 (tmm) cc_final: 0.8407 (tmm) REVERT: A 543 MET cc_start: 0.8671 (ppp) cc_final: 0.7779 (ppp) REVERT: B 116 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.5809 (t80) REVERT: B 335 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.8834 (tp30) REVERT: B 439 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8653 (ttpp) REVERT: C 179 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9363 (tt) REVERT: C 184 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.8716 (t60) REVERT: C 424 MET cc_start: 0.8420 (tmm) cc_final: 0.8007 (tmm) REVERT: C 577 GLN cc_start: 0.9504 (OUTLIER) cc_final: 0.8992 (mt0) outliers start: 72 outliers final: 50 residues processed: 126 average time/residue: 0.0980 time to fit residues: 20.7287 Evaluate side-chains 114 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 58 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 653 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 113 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 136 optimal weight: 30.0000 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.043997 restraints weight = 87858.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.045362 restraints weight = 51863.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.046339 restraints weight = 36896.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.047030 restraints weight = 29269.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.047478 restraints weight = 25007.706| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16677 Z= 0.113 Angle : 0.543 9.947 22572 Z= 0.271 Chirality : 0.043 0.141 2634 Planarity : 0.004 0.057 2931 Dihedral : 4.003 24.143 2293 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.53 % Allowed : 28.64 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 2124 helix: 2.66 (0.19), residues: 734 sheet: 0.54 (0.23), residues: 504 loop : -0.90 (0.23), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 749 TYR 0.014 0.001 TYR B 334 PHE 0.013 0.001 PHE A 545 TRP 0.002 0.001 TRP C 184 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00245 (16677) covalent geometry : angle 0.54336 (22572) hydrogen bonds : bond 0.03619 ( 888) hydrogen bonds : angle 4.50415 ( 2454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 58 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8415 (tmm) cc_final: 0.8168 (tmm) REVERT: A 228 MET cc_start: 0.8717 (tmm) cc_final: 0.8412 (tmm) REVERT: A 439 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8266 (ptmm) REVERT: A 543 MET cc_start: 0.8695 (ppp) cc_final: 0.7772 (ppp) REVERT: B 116 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.5694 (t80) REVERT: B 184 TRP cc_start: 0.9110 (OUTLIER) cc_final: 0.8482 (t60) REVERT: B 335 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8850 (tp30) REVERT: B 439 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8628 (ttpp) REVERT: C 104 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8521 (tp-100) REVERT: C 179 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9295 (tt) REVERT: C 184 TRP cc_start: 0.9095 (OUTLIER) cc_final: 0.8620 (t60) REVERT: C 424 MET cc_start: 0.8435 (tmm) cc_final: 0.8002 (tmm) REVERT: C 577 GLN cc_start: 0.9484 (OUTLIER) cc_final: 0.8976 (mt0) outliers start: 64 outliers final: 45 residues processed: 118 average time/residue: 0.1159 time to fit residues: 22.7562 Evaluate side-chains 112 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 58 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 TRP Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 653 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 129 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 137 optimal weight: 40.0000 chunk 208 optimal weight: 20.0000 chunk 135 optimal weight: 40.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.065837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.043829 restraints weight = 88013.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.045179 restraints weight = 52203.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.046162 restraints weight = 37389.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.046722 restraints weight = 29860.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.047203 restraints weight = 25630.268| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16677 Z= 0.134 Angle : 0.544 9.483 22572 Z= 0.271 Chirality : 0.042 0.149 2634 Planarity : 0.004 0.054 2931 Dihedral : 3.966 26.525 2293 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.37 % Allowed : 28.70 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.19), residues: 2124 helix: 2.68 (0.19), residues: 734 sheet: 0.57 (0.24), residues: 504 loop : -0.87 (0.23), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 749 TYR 0.015 0.001 TYR B 334 PHE 0.011 0.001 PHE A 545 TRP 0.002 0.001 TRP B 184 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00294 (16677) covalent geometry : angle 0.54378 (22572) hydrogen bonds : bond 0.03541 ( 888) hydrogen bonds : angle 4.46151 ( 2454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 59 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8438 (tmm) cc_final: 0.8179 (tmm) REVERT: A 228 MET cc_start: 0.8702 (tmm) cc_final: 0.8422 (tmm) REVERT: A 439 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8286 (ptmm) REVERT: A 543 MET cc_start: 0.8716 (ppp) cc_final: 0.7789 (ppp) REVERT: B 44 MET cc_start: 0.5221 (tpt) cc_final: 0.4698 (mmp) REVERT: B 116 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.5725 (t80) REVERT: B 184 TRP cc_start: 0.9124 (OUTLIER) cc_final: 0.8555 (t60) REVERT: B 335 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8809 (tp30) REVERT: B 439 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8639 (ttpp) REVERT: C 179 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9297 (tt) REVERT: C 184 TRP cc_start: 0.9117 (OUTLIER) cc_final: 0.8638 (t60) REVERT: C 209 MET cc_start: 0.9342 (mmm) cc_final: 0.8921 (mpp) REVERT: C 424 MET cc_start: 0.8434 (tmm) cc_final: 0.7989 (tmm) REVERT: C 577 GLN cc_start: 0.9480 (OUTLIER) cc_final: 0.8981 (mt0) outliers start: 61 outliers final: 49 residues processed: 114 average time/residue: 0.1128 time to fit residues: 21.2074 Evaluate side-chains 115 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 58 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 TRP Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 653 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 210 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 135 optimal weight: 40.0000 chunk 4 optimal weight: 0.0030 chunk 56 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.043885 restraints weight = 88317.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.045264 restraints weight = 52314.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.046188 restraints weight = 37199.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.046890 restraints weight = 29567.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.047259 restraints weight = 25473.946| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16677 Z= 0.133 Angle : 0.558 11.817 22572 Z= 0.274 Chirality : 0.042 0.150 2634 Planarity : 0.003 0.054 2931 Dihedral : 3.960 27.181 2293 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.64 % Allowed : 28.70 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.19), residues: 2124 helix: 2.71 (0.19), residues: 734 sheet: 0.60 (0.24), residues: 505 loop : -0.87 (0.23), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 119 TYR 0.014 0.001 TYR B 334 PHE 0.011 0.001 PHE A 545 TRP 0.002 0.001 TRP C 184 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00291 (16677) covalent geometry : angle 0.55778 (22572) hydrogen bonds : bond 0.03510 ( 888) hydrogen bonds : angle 4.40720 ( 2454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 61 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8700 (tmm) cc_final: 0.8453 (tmm) REVERT: A 439 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8291 (ptmm) REVERT: A 543 MET cc_start: 0.8683 (ppp) cc_final: 0.7753 (ppp) REVERT: B 44 MET cc_start: 0.5221 (tpt) cc_final: 0.4706 (mmp) REVERT: B 49 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9084 (p) REVERT: B 116 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.5737 (t80) REVERT: B 184 TRP cc_start: 0.9117 (OUTLIER) cc_final: 0.8545 (t60) REVERT: B 209 MET cc_start: 0.9341 (tpp) cc_final: 0.9044 (mpp) REVERT: B 335 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.8828 (tp30) REVERT: B 439 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8665 (ttpp) REVERT: C 96 MET cc_start: 0.9151 (mmm) cc_final: 0.8735 (tmm) REVERT: C 179 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9319 (tt) REVERT: C 184 TRP cc_start: 0.9122 (OUTLIER) cc_final: 0.8647 (t60) REVERT: C 424 MET cc_start: 0.8435 (tmm) cc_final: 0.7974 (tmm) REVERT: C 577 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.8982 (mt0) outliers start: 66 outliers final: 54 residues processed: 122 average time/residue: 0.1165 time to fit residues: 23.6078 Evaluate side-chains 121 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 58 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 TRP Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 304 HIS Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 653 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 118 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.0000 chunk 151 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.065111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.039369 restraints weight = 81938.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.040401 restraints weight = 52171.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.041534 restraints weight = 39777.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.041938 restraints weight = 33248.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.042377 restraints weight = 30063.521| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16677 Z= 0.121 Angle : 0.554 10.912 22572 Z= 0.272 Chirality : 0.043 0.170 2634 Planarity : 0.003 0.054 2931 Dihedral : 3.923 29.617 2293 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.48 % Allowed : 29.14 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.19), residues: 2124 helix: 2.74 (0.19), residues: 734 sheet: 0.63 (0.24), residues: 505 loop : -0.85 (0.23), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 749 TYR 0.014 0.001 TYR B 334 PHE 0.011 0.001 PHE A 545 TRP 0.002 0.001 TRP B 184 HIS 0.004 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00267 (16677) covalent geometry : angle 0.55382 (22572) hydrogen bonds : bond 0.03403 ( 888) hydrogen bonds : angle 4.34876 ( 2454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 60 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8710 (tmm) cc_final: 0.8441 (tmm) REVERT: A 439 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8303 (ptmm) REVERT: A 485 MET cc_start: 0.9039 (mmp) cc_final: 0.8737 (mmp) REVERT: A 543 MET cc_start: 0.8647 (ppp) cc_final: 0.7689 (ppp) REVERT: B 44 MET cc_start: 0.5248 (tpt) cc_final: 0.4753 (mmp) REVERT: B 49 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9131 (p) REVERT: B 116 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.5820 (t80) REVERT: B 184 TRP cc_start: 0.9086 (OUTLIER) cc_final: 0.8517 (t60) REVERT: B 209 MET cc_start: 0.9289 (tpp) cc_final: 0.9004 (mpp) REVERT: B 335 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9001 (tp30) REVERT: B 439 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8664 (ttpt) REVERT: C 96 MET cc_start: 0.9208 (mmm) cc_final: 0.8917 (tpp) REVERT: C 179 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9288 (tt) REVERT: C 184 TRP cc_start: 0.9093 (OUTLIER) cc_final: 0.8610 (t60) REVERT: C 424 MET cc_start: 0.8426 (tmm) cc_final: 0.7964 (tmm) REVERT: C 577 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.9009 (mt0) outliers start: 63 outliers final: 50 residues processed: 118 average time/residue: 0.1152 time to fit residues: 22.3739 Evaluate side-chains 117 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 58 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 TRP Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 154 CYS Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 304 HIS Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 401 SER Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 653 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 44 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 194 optimal weight: 0.2980 chunk 70 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 0.4980 chunk 148 optimal weight: 0.0770 chunk 184 optimal weight: 0.7980 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.076325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.049163 restraints weight = 95121.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050360 restraints weight = 58101.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051952 restraints weight = 43727.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.052461 restraints weight = 36367.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.052649 restraints weight = 33037.751| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16677 Z= 0.101 Angle : 0.568 11.098 22572 Z= 0.276 Chirality : 0.043 0.167 2634 Planarity : 0.003 0.052 2931 Dihedral : 3.899 32.107 2293 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.65 % Allowed : 29.80 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.19), residues: 2124 helix: 2.70 (0.19), residues: 735 sheet: 0.71 (0.24), residues: 502 loop : -0.80 (0.23), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 746 TYR 0.013 0.001 TYR A 334 PHE 0.013 0.001 PHE A 545 TRP 0.002 0.001 TRP A 184 HIS 0.004 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00222 (16677) covalent geometry : angle 0.56787 (22572) hydrogen bonds : bond 0.03237 ( 888) hydrogen bonds : angle 4.29232 ( 2454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 59 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8690 (tmm) cc_final: 0.8446 (tmm) REVERT: A 439 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8345 (ptmm) REVERT: A 543 MET cc_start: 0.8626 (ppp) cc_final: 0.7671 (ppp) REVERT: B 44 MET cc_start: 0.5145 (tpt) cc_final: 0.4654 (mmp) REVERT: B 116 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.5730 (t80) REVERT: B 184 TRP cc_start: 0.9004 (OUTLIER) cc_final: 0.8529 (t60) REVERT: B 335 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.8765 (tp30) REVERT: B 439 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8661 (ttpt) REVERT: C 96 MET cc_start: 0.9203 (mmm) cc_final: 0.8910 (tpp) REVERT: C 179 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9250 (tt) REVERT: C 424 MET cc_start: 0.8406 (tmm) cc_final: 0.7932 (tmm) outliers start: 48 outliers final: 41 residues processed: 103 average time/residue: 0.1116 time to fit residues: 19.3171 Evaluate side-chains 105 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 58 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 733 VAL Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 184 TRP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 423 PHE Chi-restraints excluded: chain B residue 439 LYS Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 703 THR Chi-restraints excluded: chain B residue 717 ILE Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 733 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 304 HIS Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 653 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 97 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN B 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045801 restraints weight = 96642.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.047305 restraints weight = 59716.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048752 restraints weight = 45301.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049048 restraints weight = 37981.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.049366 restraints weight = 34814.007| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16677 Z= 0.261 Angle : 0.637 10.121 22572 Z= 0.314 Chirality : 0.043 0.181 2634 Planarity : 0.004 0.057 2931 Dihedral : 4.030 31.499 2293 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.37 % Allowed : 29.14 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.19), residues: 2124 helix: 2.65 (0.19), residues: 734 sheet: 0.63 (0.24), residues: 503 loop : -0.91 (0.23), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 119 TYR 0.014 0.001 TYR B 334 PHE 0.007 0.001 PHE B 241 TRP 0.005 0.001 TRP B 184 HIS 0.004 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00568 (16677) covalent geometry : angle 0.63718 (22572) hydrogen bonds : bond 0.03789 ( 888) hydrogen bonds : angle 4.56375 ( 2454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.93 seconds wall clock time: 49 minutes 14.60 seconds (2954.60 seconds total)