Starting phenix.real_space_refine on Sat Jun 14 21:43:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kjr_62372/06_2025/9kjr_62372.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kjr_62372/06_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_62372/06_2025/9kjr_62372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kjr_62372/06_2025/9kjr_62372.map" model { file = "/net/cci-nas-00/data/ceres_data/9kjr_62372/06_2025/9kjr_62372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kjr_62372/06_2025/9kjr_62372.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.04, per 1000 atoms: 0.67 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: 4.30 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.14 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: 6.75 Time building geometry restraints manager: 5.14 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: 0.05 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: 2.540 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.810 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (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 TRP 0.007 0.002 TRP B 184 HIS 0.005 0.001 HIS B 708 PHE 0.010 0.001 PHE B 736 TYR 0.016 0.001 TYR B 334 ARG 0.008 0.000 ARG A 749 Details of bonding type rmsd hydrogen bonds : bond 0.13266 ( 888) hydrogen bonds : angle 6.16794 ( 2454) covalent geometry : bond 0.00474 (16677) covalent geometry : angle 0.62692 (22572) *********************** 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 : 1.703 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: 0.2553 time to fit residues: 27.4020 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 : 1.952 ------------------------------------------------------------------------------- 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 179 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 392 GLN C 632 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.042474 restraints weight = 87884.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.043758 restraints weight = 53279.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.044664 restraints weight = 38621.304| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16677 Z= 0.234 Angle : 0.589 7.040 22572 Z= 0.305 Chirality : 0.043 0.140 2634 Planarity : 0.004 0.060 2931 Dihedral : 4.197 27.994 2294 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.98 % Allowed : 28.48 % Favored : 68.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2124 helix: 2.44 (0.19), residues: 732 sheet: 0.44 (0.23), residues: 502 loop : -0.94 (0.23), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.004 0.001 HIS A 304 PHE 0.011 0.001 PHE A 545 TYR 0.017 0.001 TYR B 334 ARG 0.007 0.001 ARG A 749 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 888) hydrogen bonds : angle 5.16730 ( 2454) covalent geometry : bond 0.00506 (16677) covalent geometry : angle 0.58921 (22572) *********************** 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 114 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 60 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 MET cc_start: 0.9294 (tpt) cc_final: 0.8720 (tpp) REVERT: B 116 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6154 (t80) REVERT: C 184 TRP cc_start: 0.9202 (OUTLIER) cc_final: 0.8743 (t60) REVERT: C 209 MET cc_start: 0.9224 (mpp) cc_final: 0.8833 (mpp) REVERT: C 424 MET cc_start: 0.8382 (tmm) cc_final: 0.8144 (tmm) REVERT: C 577 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.9036 (mt0) REVERT: C 695 MET cc_start: 0.1782 (tpt) cc_final: 0.1525 (tpp) outliers start: 54 outliers final: 32 residues processed: 110 average time/residue: 0.2436 time to fit residues: 43.9821 Evaluate side-chains 92 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 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 377 PHE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 681 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 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 75 SER Chi-restraints excluded: chain C residue 78 THR 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 213 THR 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 653 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 178 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 116 optimal weight: 0.0270 chunk 86 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.064860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.039363 restraints weight = 81052.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.040509 restraints weight = 51537.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.041278 restraints weight = 38865.893| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16677 Z= 0.115 Angle : 0.523 6.967 22572 Z= 0.270 Chirality : 0.043 0.142 2634 Planarity : 0.004 0.057 2931 Dihedral : 4.052 22.778 2293 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.98 % Allowed : 28.53 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 2124 helix: 2.57 (0.19), residues: 738 sheet: 0.50 (0.23), residues: 503 loop : -0.88 (0.23), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.005 0.001 HIS A 304 PHE 0.014 0.001 PHE A 545 TYR 0.015 0.001 TYR B 334 ARG 0.012 0.000 ARG C 749 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 888) hydrogen bonds : angle 4.73815 ( 2454) covalent geometry : bond 0.00242 (16677) covalent geometry : angle 0.52321 (22572) *********************** 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 113 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 59 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8475 (tmm) cc_final: 0.8256 (tmm) REVERT: A 228 MET cc_start: 0.8801 (tmm) cc_final: 0.8406 (tmm) REVERT: A 496 MET cc_start: 0.9245 (tpt) cc_final: 0.9029 (tpp) REVERT: A 543 MET cc_start: 0.8608 (ppp) cc_final: 0.7793 (ppp) REVERT: B 116 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 439 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8598 (ttpp) REVERT: C 104 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: C 209 MET cc_start: 0.9158 (tpp) cc_final: 0.8637 (mpp) REVERT: C 424 MET cc_start: 0.8414 (tmm) cc_final: 0.8058 (tmm) REVERT: C 577 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.9003 (mt0) REVERT: C 675 GLN cc_start: 0.5648 (OUTLIER) cc_final: 0.5282 (mm110) outliers start: 54 outliers final: 30 residues processed: 108 average time/residue: 0.2875 time to fit residues: 49.1208 Evaluate side-chains 93 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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 188 VAL Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 367 LEU 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 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 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 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 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 104 GLN 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 675 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 114 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** 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 = 0.3236 r_free = 0.3236 target = 0.063741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.042704 restraints weight = 86766.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.043981 restraints weight = 52390.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.044890 restraints weight = 37748.620| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16677 Z= 0.206 Angle : 0.567 7.876 22572 Z= 0.289 Chirality : 0.043 0.213 2634 Planarity : 0.004 0.073 2931 Dihedral : 4.080 23.472 2293 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.48 % Allowed : 28.64 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2124 helix: 2.51 (0.19), residues: 739 sheet: 0.46 (0.23), residues: 504 loop : -0.95 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.003 0.001 HIS B 426 PHE 0.011 0.001 PHE A 545 TYR 0.016 0.001 TYR B 334 ARG 0.005 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 888) hydrogen bonds : angle 4.75647 ( 2454) covalent geometry : bond 0.00448 (16677) covalent geometry : angle 0.56746 (22572) *********************** 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 : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8753 (tmm) cc_final: 0.8393 (tmm) REVERT: A 543 MET cc_start: 0.8682 (ppp) cc_final: 0.7818 (ppp) REVERT: B 116 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.6323 (t80) REVERT: B 426 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7736 (t-170) REVERT: B 439 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8662 (ttpp) REVERT: C 184 TRP cc_start: 0.9193 (OUTLIER) cc_final: 0.8693 (t60) REVERT: C 424 MET cc_start: 0.8452 (tmm) cc_final: 0.8060 (tmm) REVERT: C 577 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.9008 (mt0) outliers start: 63 outliers final: 42 residues processed: 116 average time/residue: 0.2488 time to fit residues: 47.2337 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 : 2.027 ------------------------------------------------------------------------------- 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 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 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 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 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 653 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 717 ILE 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 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 504 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 646 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 135 optimal weight: 50.0000 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.038783 restraints weight = 82699.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.039937 restraints weight = 52520.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.040681 restraints weight = 39526.236| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16677 Z= 0.149 Angle : 0.542 8.099 22572 Z= 0.275 Chirality : 0.043 0.190 2634 Planarity : 0.004 0.059 2931 Dihedral : 4.058 22.799 2293 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.20 % Allowed : 29.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 2124 helix: 2.54 (0.19), residues: 739 sheet: 0.47 (0.23), residues: 504 loop : -0.93 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.004 0.001 HIS A 304 PHE 0.012 0.001 PHE A 545 TYR 0.015 0.001 TYR B 334 ARG 0.004 0.000 ARG A 749 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 888) hydrogen bonds : angle 4.64005 ( 2454) covalent geometry : bond 0.00324 (16677) covalent geometry : angle 0.54172 (22572) *********************** 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 118 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 60 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8768 (tmm) cc_final: 0.8467 (tmm) REVERT: A 496 MET cc_start: 0.9299 (tpp) cc_final: 0.9041 (tpp) REVERT: A 543 MET cc_start: 0.8690 (ppp) cc_final: 0.7792 (ppp) REVERT: B 116 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.5961 (t80) REVERT: B 335 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.8873 (tp30) REVERT: B 426 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7798 (t-170) REVERT: B 439 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8601 (ttpp) REVERT: C 184 TRP cc_start: 0.9147 (OUTLIER) cc_final: 0.8663 (t60) REVERT: C 424 MET cc_start: 0.8445 (tmm) cc_final: 0.8032 (tmm) REVERT: C 577 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.9035 (mt0) outliers start: 58 outliers final: 43 residues processed: 113 average time/residue: 0.2336 time to fit residues: 44.2679 Evaluate side-chains 107 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 58 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 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 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 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 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 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 593 ILE 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 154 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.063977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.042853 restraints weight = 87100.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.044192 restraints weight = 52361.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.045144 restraints weight = 37548.198| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1129 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= 0.172 Angle : 0.558 9.423 22572 Z= 0.280 Chirality : 0.043 0.152 2634 Planarity : 0.004 0.059 2931 Dihedral : 4.059 24.034 2293 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.75 % Allowed : 29.42 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 2124 helix: 2.55 (0.19), residues: 739 sheet: 0.48 (0.24), residues: 504 loop : -0.93 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.004 0.001 HIS A 304 PHE 0.011 0.001 PHE A 545 TYR 0.015 0.001 TYR B 334 ARG 0.004 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 888) hydrogen bonds : angle 4.61738 ( 2454) covalent geometry : bond 0.00375 (16677) covalent geometry : angle 0.55792 (22572) *********************** 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 126 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 58 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8471 (tmm) cc_final: 0.8237 (tmm) REVERT: A 228 MET cc_start: 0.8767 (tmm) cc_final: 0.8494 (tmm) REVERT: A 543 MET cc_start: 0.8699 (ppp) cc_final: 0.7770 (ppp) REVERT: B 49 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9114 (p) REVERT: B 116 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.5916 (t80) REVERT: B 184 TRP cc_start: 0.9202 (OUTLIER) cc_final: 0.8514 (t60) REVERT: B 335 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.9099 (tp30) REVERT: B 439 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8628 (ttpt) REVERT: C 184 TRP cc_start: 0.9172 (OUTLIER) cc_final: 0.8706 (t60) REVERT: C 424 MET cc_start: 0.8473 (tmm) cc_final: 0.8044 (tmm) REVERT: C 577 GLN cc_start: 0.9502 (OUTLIER) cc_final: 0.9000 (mt0) outliers start: 68 outliers final: 51 residues processed: 121 average time/residue: 0.2332 time to fit residues: 47.1047 Evaluate side-chains 116 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 58 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 229 LEU 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 378 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 566 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 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 593 ILE Chi-restraints excluded: chain B residue 653 THR 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 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 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 504 SER Chi-restraints excluded: chain C residue 577 GLN Chi-restraints excluded: chain C residue 585 ILE 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 104 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 201 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.064891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.038829 restraints weight = 81743.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.040110 restraints weight = 52374.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.040828 restraints weight = 39965.743| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16677 Z= 0.120 Angle : 0.534 8.293 22572 Z= 0.269 Chirality : 0.043 0.149 2634 Planarity : 0.004 0.054 2931 Dihedral : 4.005 26.311 2293 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.70 % Allowed : 29.30 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 2124 helix: 2.63 (0.19), residues: 739 sheet: 0.55 (0.24), residues: 504 loop : -0.86 (0.23), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.004 0.001 HIS A 304 PHE 0.012 0.001 PHE A 545 TYR 0.015 0.001 TYR B 334 ARG 0.003 0.000 ARG A 749 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 888) hydrogen bonds : angle 4.48014 ( 2454) covalent geometry : bond 0.00261 (16677) covalent geometry : angle 0.53386 (22572) *********************** 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 126 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 59 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8390 (tmm) cc_final: 0.8180 (tmm) REVERT: A 228 MET cc_start: 0.8739 (tmm) cc_final: 0.8505 (tmm) REVERT: A 496 MET cc_start: 0.9196 (tpt) cc_final: 0.8775 (tpp) REVERT: A 543 MET cc_start: 0.8685 (ppp) cc_final: 0.7741 (ppp) REVERT: B 44 MET cc_start: 0.5337 (tpt) cc_final: 0.4825 (mmp) REVERT: B 116 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.5948 (t80) REVERT: B 184 TRP cc_start: 0.9108 (OUTLIER) cc_final: 0.8529 (t60) REVERT: B 335 GLU cc_start: 0.9407 (OUTLIER) cc_final: 0.9098 (tp30) REVERT: B 439 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8664 (ttpp) REVERT: C 184 TRP cc_start: 0.9098 (OUTLIER) cc_final: 0.8623 (t60) REVERT: C 209 MET cc_start: 0.9292 (mmm) cc_final: 0.8911 (mpp) REVERT: C 424 MET cc_start: 0.8476 (tmm) cc_final: 0.8035 (tmm) REVERT: C 577 GLN cc_start: 0.9505 (OUTLIER) cc_final: 0.9041 (mt0) outliers start: 67 outliers final: 52 residues processed: 121 average time/residue: 0.3002 time to fit residues: 61.3084 Evaluate side-chains 116 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 58 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 332 ASP Chi-restraints excluded: chain A residue 367 LEU 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 503 SER 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 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 593 ILE Chi-restraints excluded: chain B residue 653 THR 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 75 SER 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 184 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 65 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.064176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.039015 restraints weight = 81737.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.040006 restraints weight = 52032.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.040784 restraints weight = 40052.783| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16677 Z= 0.168 Angle : 0.567 10.294 22572 Z= 0.280 Chirality : 0.043 0.147 2634 Planarity : 0.004 0.056 2931 Dihedral : 4.009 27.426 2293 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.75 % Allowed : 29.30 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2124 helix: 2.67 (0.19), residues: 733 sheet: 0.56 (0.24), residues: 504 loop : -0.90 (0.23), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.003 0.001 HIS A 304 PHE 0.009 0.001 PHE A 545 TYR 0.015 0.001 TYR B 334 ARG 0.004 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 888) hydrogen bonds : angle 4.50864 ( 2454) covalent geometry : bond 0.00368 (16677) covalent geometry : angle 0.56736 (22572) *********************** 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: 68 poor density : 59 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8773 (tmm) cc_final: 0.8539 (tmm) REVERT: A 439 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8294 (ptmm) REVERT: A 543 MET cc_start: 0.8664 (ppp) cc_final: 0.7698 (ppp) REVERT: B 44 MET cc_start: 0.5456 (tpt) cc_final: 0.4954 (mmp) REVERT: B 49 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9175 (m) REVERT: B 116 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6032 (t80) REVERT: B 184 TRP cc_start: 0.9149 (OUTLIER) cc_final: 0.8510 (t60) REVERT: B 335 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9004 (tp30) REVERT: B 439 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8687 (ttpp) REVERT: C 184 TRP cc_start: 0.9147 (OUTLIER) cc_final: 0.8671 (t60) REVERT: C 424 MET cc_start: 0.8489 (tmm) cc_final: 0.8021 (tmm) REVERT: C 577 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.9056 (mt0) outliers start: 68 outliers final: 57 residues processed: 121 average time/residue: 0.2875 time to fit residues: 58.4720 Evaluate side-chains 123 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 58 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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 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 503 SER 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 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 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 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 365 THR 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 104 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.063987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.042902 restraints weight = 86749.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.044193 restraints weight = 52533.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.045130 restraints weight = 38103.041| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16677 Z= 0.177 Angle : 0.572 9.405 22572 Z= 0.284 Chirality : 0.043 0.148 2634 Planarity : 0.004 0.057 2931 Dihedral : 4.036 29.577 2293 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.86 % Allowed : 29.08 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2124 helix: 2.67 (0.19), residues: 733 sheet: 0.56 (0.24), residues: 504 loop : -0.90 (0.23), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.003 0.001 HIS A 304 PHE 0.009 0.001 PHE A 545 TYR 0.015 0.001 TYR B 334 ARG 0.004 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 888) hydrogen bonds : angle 4.51725 ( 2454) covalent geometry : bond 0.00385 (16677) covalent geometry : angle 0.57164 (22572) *********************** 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 129 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 59 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8730 (tmm) cc_final: 0.8517 (tmm) REVERT: A 543 MET cc_start: 0.8682 (ppp) cc_final: 0.7725 (ppp) REVERT: B 44 MET cc_start: 0.5345 (tpt) cc_final: 0.4839 (mmp) REVERT: B 49 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9134 (m) REVERT: B 184 TRP cc_start: 0.9167 (OUTLIER) cc_final: 0.8536 (t60) REVERT: B 335 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9012 (tp30) REVERT: B 439 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8667 (ttpt) REVERT: C 96 MET cc_start: 0.9140 (mmm) cc_final: 0.8726 (tmm) REVERT: C 184 TRP cc_start: 0.9168 (OUTLIER) cc_final: 0.8693 (t60) REVERT: C 209 MET cc_start: 0.9434 (mmm) cc_final: 0.9223 (mmm) REVERT: C 424 MET cc_start: 0.8472 (tmm) cc_final: 0.8040 (tmm) REVERT: C 577 GLN cc_start: 0.9499 (OUTLIER) cc_final: 0.9026 (mt0) outliers start: 70 outliers final: 61 residues processed: 123 average time/residue: 0.2845 time to fit residues: 58.6589 Evaluate side-chains 125 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 58 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 280 SER 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 378 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 588 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 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 593 ILE Chi-restraints excluded: chain B residue 653 THR 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 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 365 THR 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 585 ILE 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 4 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 209 optimal weight: 0.3980 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.066827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.044685 restraints weight = 87911.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.046097 restraints weight = 52402.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.047106 restraints weight = 37300.184| |-----------------------------------------------------------------------------| r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16677 Z= 0.101 Angle : 0.564 10.297 22572 Z= 0.276 Chirality : 0.043 0.148 2634 Planarity : 0.004 0.055 2931 Dihedral : 3.973 31.760 2293 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.92 % Allowed : 30.02 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 2124 helix: 2.70 (0.19), residues: 735 sheet: 0.64 (0.24), residues: 505 loop : -0.81 (0.23), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 184 HIS 0.005 0.001 HIS A 304 PHE 0.015 0.001 PHE A 545 TYR 0.014 0.001 TYR A 334 ARG 0.004 0.000 ARG B 746 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 888) hydrogen bonds : angle 4.32463 ( 2454) covalent geometry : bond 0.00216 (16677) covalent geometry : angle 0.56432 (22572) ********************** 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 115 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 62 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8727 (tmm) cc_final: 0.8473 (tmm) REVERT: A 439 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8318 (ptmm) REVERT: A 485 MET cc_start: 0.9083 (mmp) cc_final: 0.8815 (mmp) REVERT: A 543 MET cc_start: 0.8659 (ppp) cc_final: 0.7704 (ppp) REVERT: B 44 MET cc_start: 0.5315 (tpt) cc_final: 0.4831 (mmp) REVERT: B 335 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.8859 (tp30) REVERT: B 439 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8655 (ttpt) REVERT: C 96 MET cc_start: 0.9210 (mmm) cc_final: 0.8714 (tmm) REVERT: C 424 MET cc_start: 0.8485 (tmm) cc_final: 0.8028 (tmm) outliers start: 53 outliers final: 47 residues processed: 110 average time/residue: 0.3341 time to fit residues: 60.1792 Evaluate side-chains 108 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 58 time to evaluate : 1.988 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 310 ASP 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 503 SER 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 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 B residue 733 VAL Chi-restraints excluded: chain C residue 44 MET 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 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 612 VAL Chi-restraints excluded: chain C residue 646 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 105 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 55 optimal weight: 0.0980 chunk 181 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 141 optimal weight: 40.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.064024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.038305 restraints weight = 82525.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.039514 restraints weight = 53528.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.040198 restraints weight = 40608.893| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16677 Z= 0.209 Angle : 0.602 10.729 22572 Z= 0.296 Chirality : 0.043 0.233 2634 Planarity : 0.004 0.058 2931 Dihedral : 4.002 31.151 2293 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.15 % Allowed : 29.97 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 2124 helix: 2.65 (0.19), residues: 733 sheet: 0.62 (0.24), residues: 505 loop : -0.86 (0.23), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 184 HIS 0.003 0.001 HIS B 243 PHE 0.007 0.001 PHE A 545 TYR 0.014 0.001 TYR B 334 ARG 0.004 0.000 ARG C 119 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 888) hydrogen bonds : angle 4.51070 ( 2454) covalent geometry : bond 0.00459 (16677) covalent geometry : angle 0.60191 (22572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.38 seconds wall clock time: 89 minutes 36.46 seconds (5376.46 seconds total)