Starting phenix.real_space_refine on Wed Feb 4 18:04:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mbd_63774/02_2026/9mbd_63774_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mbd_63774/02_2026/9mbd_63774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mbd_63774/02_2026/9mbd_63774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mbd_63774/02_2026/9mbd_63774.map" model { file = "/net/cci-nas-00/data/ceres_data/9mbd_63774/02_2026/9mbd_63774_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mbd_63774/02_2026/9mbd_63774_neut.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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 80 5.16 5 C 7660 2.51 5 N 2006 2.21 5 O 2189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11935 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5964 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 732} Chain breaks: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 5971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5971 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 38, 'TRANS': 732} Chain breaks: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 2.79, per 1000 atoms: 0.23 Number of scatterers: 11935 At special positions: 0 Unit cell: (91.5, 109.5, 195, 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 80 16.00 O 2189 8.00 N 2006 7.00 C 7660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 424 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 538 " distance=2.03 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 553 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 516 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 553 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 569 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 742 " distance=2.04 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: 0.92 Conformation dependent library (CDL) restraints added in 696.7 milliseconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2876 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 45.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 72 through 87 removed outlier: 3.650A pdb=" N ALA A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 120 removed outlier: 3.908A pdb=" N GLU A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 removed outlier: 3.566A pdb=" N ILE A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 201 through 214 removed outlier: 4.118A pdb=" N ALA A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 243 removed outlier: 3.947A pdb=" N GLU A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.175A pdb=" N GLU A 326 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.681A pdb=" N VAL A 402 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 403 " --> pdb=" O GLY A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 403' Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.601A pdb=" N ALA A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 584 through 608 removed outlier: 3.833A pdb=" N VAL A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.824A pdb=" N ALA A 616 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 640 removed outlier: 3.500A pdb=" N TYR A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 678 removed outlier: 4.487A pdb=" N ARG A 652 " --> pdb=" O CYS A 648 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.766A pdb=" N GLN A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 removed outlier: 3.953A pdb=" N LEU A 749 " --> pdb=" O SER A 745 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 802 removed outlier: 3.810A pdb=" N GLY A 784 " --> pdb=" O ALA A 780 " (cutoff:3.500A) Proline residue: A 799 - end of helix Processing helix chain 'A' and resid 812 through 832 removed outlier: 3.906A pdb=" N THR A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.650A pdb=" N ALA B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.908A pdb=" N GLU B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 168 removed outlier: 3.566A pdb=" N ILE B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 201 through 214 removed outlier: 4.119A pdb=" N ALA B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 214 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.947A pdb=" N GLU B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 322 through 326 removed outlier: 4.176A pdb=" N GLU B 326 " --> pdb=" O GLU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 399 through 403 removed outlier: 3.681A pdb=" N VAL B 402 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN B 403 " --> pdb=" O GLY B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 403' Processing helix chain 'B' and resid 404 through 421 removed outlier: 3.600A pdb=" N ALA B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 584 through 608 removed outlier: 3.833A pdb=" N VAL B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 617 removed outlier: 3.825A pdb=" N ALA B 616 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 640 removed outlier: 3.500A pdb=" N TYR B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 678 removed outlier: 4.488A pdb=" N ARG B 652 " --> pdb=" O CYS B 648 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 700 Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.767A pdb=" N GLN B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 770 removed outlier: 3.954A pdb=" N LEU B 749 " --> pdb=" O SER B 745 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 770 " --> pdb=" O TYR B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 802 removed outlier: 3.810A pdb=" N GLY B 784 " --> pdb=" O ALA B 780 " (cutoff:3.500A) Proline residue: B 799 - end of helix Processing helix chain 'B' and resid 812 through 832 removed outlier: 3.907A pdb=" N THR B 816 " --> pdb=" O TYR B 812 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.877A pdb=" N ARG A 101 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 48 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LEU A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY A 50 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.877A pdb=" N ARG A 101 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 48 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LEU A 103 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY A 50 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE A 47 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N ILE A 151 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY A 49 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 247 removed outlier: 4.762A pdb=" N ALA A 277 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 278 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 333 removed outlier: 3.777A pdb=" N GLY A 489 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 451 through 452 removed outlier: 3.838A pdb=" N PHE A 451 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 528 Processing sheet with id=AA7, first strand: chain 'A' and resid 545 through 547 Processing sheet with id=AA8, first strand: chain 'A' and resid 561 through 562 Processing sheet with id=AA9, first strand: chain 'B' and resid 40 through 41 removed outlier: 7.878A pdb=" N ARG B 101 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 48 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LEU B 103 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY B 50 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 40 through 41 removed outlier: 7.878A pdb=" N ARG B 101 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 48 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LEU B 103 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY B 50 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 47 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N ILE B 151 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY B 49 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 246 through 247 removed outlier: 4.762A pdb=" N ALA B 277 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 278 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.778A pdb=" N GLY B 489 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.838A pdb=" N PHE B 451 " --> pdb=" O VAL B 459 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 524 through 528 Processing sheet with id=AB6, first strand: chain 'B' and resid 545 through 547 Processing sheet with id=AB7, first strand: chain 'B' and resid 561 through 562 480 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3834 1.35 - 1.47: 2869 1.47 - 1.59: 5385 1.59 - 1.71: 0 1.71 - 1.83: 114 Bond restraints: 12202 Sorted by residual: bond pdb=" N CYS B 569 " pdb=" CA CYS B 569 " ideal model delta sigma weight residual 1.462 1.486 -0.023 1.20e-02 6.94e+03 3.74e+00 bond pdb=" N CYS A 569 " pdb=" CA CYS A 569 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.20e-02 6.94e+03 3.57e+00 bond pdb=" CA ILE A 798 " pdb=" C ILE A 798 " ideal model delta sigma weight residual 1.520 1.534 -0.015 8.80e-03 1.29e+04 2.80e+00 bond pdb=" CA ILE B 798 " pdb=" CB ILE B 798 " ideal model delta sigma weight residual 1.534 1.545 -0.011 6.80e-03 2.16e+04 2.57e+00 bond pdb=" CA ILE B 798 " pdb=" C ILE B 798 " ideal model delta sigma weight residual 1.520 1.534 -0.014 8.80e-03 1.29e+04 2.46e+00 ... (remaining 12197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 15992 1.61 - 3.23: 486 3.23 - 4.84: 61 4.84 - 6.45: 35 6.45 - 8.07: 7 Bond angle restraints: 16581 Sorted by residual: angle pdb=" C SER A 94 " pdb=" CA SER A 94 " pdb=" CB SER A 94 " ideal model delta sigma weight residual 116.54 111.70 4.84 1.15e+00 7.56e-01 1.77e+01 angle pdb=" C SER B 94 " pdb=" CA SER B 94 " pdb=" CB SER B 94 " ideal model delta sigma weight residual 116.54 111.70 4.84 1.15e+00 7.56e-01 1.77e+01 angle pdb=" N GLU B 261 " pdb=" CA GLU B 261 " pdb=" C GLU B 261 " ideal model delta sigma weight residual 114.56 110.04 4.52 1.27e+00 6.20e-01 1.27e+01 angle pdb=" N GLU A 261 " pdb=" CA GLU A 261 " pdb=" C GLU A 261 " ideal model delta sigma weight residual 114.56 110.05 4.51 1.27e+00 6.20e-01 1.26e+01 angle pdb=" C VAL A 585 " pdb=" N VAL A 586 " pdb=" CA VAL A 586 " ideal model delta sigma weight residual 120.33 122.84 -2.51 8.00e-01 1.56e+00 9.84e+00 ... (remaining 16576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 6659 17.16 - 34.33: 512 34.33 - 51.49: 120 51.49 - 68.66: 16 68.66 - 85.82: 12 Dihedral angle restraints: 7319 sinusoidal: 2852 harmonic: 4467 Sorted by residual: dihedral pdb=" CB CYS B 424 " pdb=" SG CYS B 424 " pdb=" SG CYS B 431 " pdb=" CB CYS B 431 " ideal model delta sinusoidal sigma weight residual 93.00 178.82 -85.82 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS A 424 " pdb=" SG CYS A 424 " pdb=" SG CYS A 431 " pdb=" CB CYS A 431 " ideal model delta sinusoidal sigma weight residual 93.00 178.81 -85.81 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS A 556 " pdb=" SG CYS A 556 " pdb=" SG CYS A 569 " pdb=" CB CYS A 569 " ideal model delta sinusoidal sigma weight residual 93.00 170.96 -77.96 1 1.00e+01 1.00e-02 7.60e+01 ... (remaining 7316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1393 0.047 - 0.094: 407 0.094 - 0.141: 100 0.141 - 0.187: 2 0.187 - 0.234: 2 Chirality restraints: 1904 Sorted by residual: chirality pdb=" CA CYS A 569 " pdb=" N CYS A 569 " pdb=" C CYS A 569 " pdb=" CB CYS A 569 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA CYS B 569 " pdb=" N CYS B 569 " pdb=" C CYS B 569 " pdb=" CB CYS B 569 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LYS A 252 " pdb=" N LYS A 252 " pdb=" C LYS A 252 " pdb=" CB LYS A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1901 not shown) Planarity restraints: 2101 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 532 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 533 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 533 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 533 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 532 " 0.036 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 533 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 52 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 53 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 53 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 53 " 0.025 5.00e-02 4.00e+02 ... (remaining 2098 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2530 2.78 - 3.31: 11731 3.31 - 3.84: 19137 3.84 - 4.37: 21264 4.37 - 4.90: 36579 Nonbonded interactions: 91241 Sorted by model distance: nonbonded pdb=" O ASN B 609 " pdb=" NH1 ARG B 615 " model vdw 2.251 3.120 nonbonded pdb=" O ASN A 609 " pdb=" NH1 ARG A 615 " model vdw 2.251 3.120 nonbonded pdb=" O GLY A 368 " pdb=" N SER A 379 " model vdw 2.260 3.120 nonbonded pdb=" O GLY B 368 " pdb=" N SER B 379 " model vdw 2.260 3.120 nonbonded pdb=" OH TYR B 227 " pdb=" OG SER B 308 " model vdw 2.264 3.040 ... (remaining 91236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 39 through 765 or (resid 766 through 767 and (name N or na \ me CA or name C or name O or name CB )) or resid 768 through 841)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.120 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12216 Z= 0.147 Angle : 0.684 8.067 16609 Z= 0.373 Chirality : 0.045 0.234 1904 Planarity : 0.005 0.055 2101 Dihedral : 13.029 78.163 4401 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.21), residues: 1522 helix: 0.21 (0.21), residues: 626 sheet: -2.96 (0.35), residues: 168 loop : -2.90 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 343 TYR 0.014 0.001 TYR B 217 PHE 0.017 0.001 PHE A 637 TRP 0.005 0.001 TRP B 579 HIS 0.001 0.000 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00297 (12202) covalent geometry : angle 0.68070 (16581) SS BOND : bond 0.00307 ( 14) SS BOND : angle 1.77972 ( 28) hydrogen bonds : bond 0.16113 ( 476) hydrogen bonds : angle 6.13010 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 MET cc_start: 0.7891 (mtp) cc_final: 0.7668 (ttm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1247 time to fit residues: 35.2688 Evaluate side-chains 93 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 HIS B 417 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.111418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.077900 restraints weight = 40031.601| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.52 r_work: 0.3364 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12216 Z= 0.163 Angle : 0.683 14.173 16609 Z= 0.351 Chirality : 0.047 0.167 1904 Planarity : 0.005 0.055 2101 Dihedral : 4.608 17.242 1665 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.17 % Allowed : 12.20 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.21), residues: 1522 helix: 0.60 (0.21), residues: 650 sheet: -2.57 (0.35), residues: 168 loop : -2.48 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 343 TYR 0.036 0.002 TYR A 788 PHE 0.033 0.002 PHE B 661 TRP 0.005 0.001 TRP A 311 HIS 0.003 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00371 (12202) covalent geometry : angle 0.68208 (16581) SS BOND : bond 0.00364 ( 14) SS BOND : angle 1.15949 ( 28) hydrogen bonds : bond 0.04912 ( 476) hydrogen bonds : angle 4.92894 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 TYR cc_start: 0.8375 (t80) cc_final: 0.7769 (t80) REVERT: A 787 MET cc_start: 0.9519 (mmm) cc_final: 0.9043 (tmm) REVERT: A 822 MET cc_start: 0.9316 (ttp) cc_final: 0.8872 (ptt) REVERT: B 654 PHE cc_start: 0.8496 (m-80) cc_final: 0.8155 (m-80) REVERT: B 822 MET cc_start: 0.9358 (ttp) cc_final: 0.9132 (ttt) REVERT: B 832 MET cc_start: 0.5198 (mmt) cc_final: 0.4361 (tmm) outliers start: 15 outliers final: 10 residues processed: 107 average time/residue: 0.1078 time to fit residues: 16.9803 Evaluate side-chains 92 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 766 TYR Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 120 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 0.0060 chunk 19 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 173 GLN A 537 HIS B 173 GLN B 537 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.112374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075681 restraints weight = 39679.175| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.64 r_work: 0.3182 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 12216 Z= 0.337 Angle : 0.803 13.766 16609 Z= 0.425 Chirality : 0.050 0.203 1904 Planarity : 0.006 0.071 2101 Dihedral : 5.241 20.040 1665 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.87 % Allowed : 15.00 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.22), residues: 1522 helix: 0.34 (0.21), residues: 654 sheet: -2.19 (0.42), residues: 140 loop : -2.31 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 433 TYR 0.031 0.003 TYR A 476 PHE 0.038 0.003 PHE A 661 TRP 0.007 0.002 TRP A 536 HIS 0.008 0.002 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00767 (12202) covalent geometry : angle 0.80246 (16581) SS BOND : bond 0.00325 ( 14) SS BOND : angle 0.94325 ( 28) hydrogen bonds : bond 0.06226 ( 476) hydrogen bonds : angle 5.20591 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8846 (mm) REVERT: A 287 ILE cc_start: 0.8601 (mm) cc_final: 0.8232 (mt) REVERT: A 427 TYR cc_start: 0.8519 (t80) cc_final: 0.7822 (t80) REVERT: A 654 PHE cc_start: 0.8521 (m-80) cc_final: 0.8223 (m-80) REVERT: A 659 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8280 (tmm) REVERT: A 660 CYS cc_start: 0.9189 (t) cc_final: 0.8793 (m) REVERT: A 787 MET cc_start: 0.9460 (mmm) cc_final: 0.8834 (tmm) REVERT: A 822 MET cc_start: 0.9526 (ttp) cc_final: 0.9232 (ttt) REVERT: B 287 ILE cc_start: 0.8604 (mm) cc_final: 0.8235 (mt) REVERT: B 434 MET cc_start: 0.7603 (ttm) cc_final: 0.6959 (mtt) REVERT: B 654 PHE cc_start: 0.8664 (m-80) cc_final: 0.8178 (m-80) REVERT: B 659 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8008 (tmm) REVERT: B 660 CYS cc_start: 0.9134 (t) cc_final: 0.8734 (m) REVERT: B 788 TYR cc_start: 0.8972 (m-10) cc_final: 0.8691 (m-80) outliers start: 37 outliers final: 22 residues processed: 129 average time/residue: 0.0837 time to fit residues: 16.6470 Evaluate side-chains 113 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 766 TYR Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** 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 = 0.4187 r_free = 0.4187 target = 0.116058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080487 restraints weight = 39151.881| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.67 r_work: 0.3291 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12216 Z= 0.127 Angle : 0.636 11.181 16609 Z= 0.319 Chirality : 0.044 0.165 1904 Planarity : 0.004 0.055 2101 Dihedral : 4.531 15.723 1665 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.33 % Allowed : 17.09 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.22), residues: 1522 helix: 0.78 (0.21), residues: 654 sheet: -2.33 (0.37), residues: 172 loop : -1.93 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 433 TYR 0.018 0.001 TYR A 788 PHE 0.044 0.002 PHE B 785 TRP 0.005 0.001 TRP B 713 HIS 0.002 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00278 (12202) covalent geometry : angle 0.63594 (16581) SS BOND : bond 0.00228 ( 14) SS BOND : angle 0.81975 ( 28) hydrogen bonds : bond 0.04513 ( 476) hydrogen bonds : angle 4.63274 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8618 (mt) REVERT: A 427 TYR cc_start: 0.8262 (t80) cc_final: 0.7790 (t80) REVERT: A 654 PHE cc_start: 0.8415 (m-80) cc_final: 0.8051 (m-80) REVERT: A 659 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8134 (tmm) REVERT: A 787 MET cc_start: 0.9433 (mmm) cc_final: 0.8962 (tmm) REVERT: A 822 MET cc_start: 0.9533 (ttp) cc_final: 0.9242 (ttp) REVERT: A 832 MET cc_start: 0.4068 (mmt) cc_final: 0.3200 (ttm) REVERT: B 113 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8343 (mm) REVERT: B 434 MET cc_start: 0.7685 (ttm) cc_final: 0.7254 (mtt) REVERT: B 654 PHE cc_start: 0.8573 (m-80) cc_final: 0.8348 (m-80) REVERT: B 787 MET cc_start: 0.9485 (mmm) cc_final: 0.9037 (tmm) REVERT: B 788 TYR cc_start: 0.8957 (m-10) cc_final: 0.8730 (m-80) REVERT: B 832 MET cc_start: 0.4318 (mmt) cc_final: 0.3846 (ttm) outliers start: 30 outliers final: 20 residues processed: 120 average time/residue: 0.0921 time to fit residues: 16.3413 Evaluate side-chains 105 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 766 TYR Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 49 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 HIS B 164 ASN B 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.112304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.076201 restraints weight = 39582.432| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.49 r_work: 0.3196 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12216 Z= 0.276 Angle : 0.727 11.355 16609 Z= 0.375 Chirality : 0.047 0.174 1904 Planarity : 0.005 0.050 2101 Dihedral : 4.801 21.182 1665 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 3.26 % Allowed : 18.96 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.22), residues: 1522 helix: 0.58 (0.21), residues: 652 sheet: -2.13 (0.42), residues: 136 loop : -2.05 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 389 TYR 0.023 0.002 TYR A 476 PHE 0.043 0.003 PHE B 661 TRP 0.006 0.001 TRP A 311 HIS 0.005 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00635 (12202) covalent geometry : angle 0.72681 (16581) SS BOND : bond 0.00292 ( 14) SS BOND : angle 0.73446 ( 28) hydrogen bonds : bond 0.05521 ( 476) hydrogen bonds : angle 4.86756 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 287 ILE cc_start: 0.8632 (mm) cc_final: 0.8251 (mt) REVERT: A 427 TYR cc_start: 0.8570 (t80) cc_final: 0.7853 (t80) REVERT: A 654 PHE cc_start: 0.8464 (m-80) cc_final: 0.8001 (m-80) REVERT: A 657 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7128 (pp) REVERT: A 695 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8193 (pp30) REVERT: A 787 MET cc_start: 0.9487 (mmm) cc_final: 0.8921 (tmm) REVERT: A 822 MET cc_start: 0.9553 (ttp) cc_final: 0.9246 (ttp) REVERT: B 76 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8574 (mp) REVERT: B 287 ILE cc_start: 0.8632 (mm) cc_final: 0.8269 (mt) REVERT: B 654 PHE cc_start: 0.8601 (m-10) cc_final: 0.8167 (m-80) REVERT: B 787 MET cc_start: 0.9531 (mmm) cc_final: 0.8933 (tmm) REVERT: B 788 TYR cc_start: 0.8946 (m-10) cc_final: 0.8712 (m-80) REVERT: B 822 MET cc_start: 0.8678 (ppp) cc_final: 0.8465 (ppp) REVERT: B 832 MET cc_start: 0.4541 (mmt) cc_final: 0.3939 (ttm) outliers start: 42 outliers final: 26 residues processed: 122 average time/residue: 0.0901 time to fit residues: 16.9805 Evaluate side-chains 109 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 632 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 825 SER Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 127 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 0.0370 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.114705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.079018 restraints weight = 39252.742| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.64 r_work: 0.3243 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12216 Z= 0.146 Angle : 0.643 10.872 16609 Z= 0.322 Chirality : 0.044 0.156 1904 Planarity : 0.004 0.050 2101 Dihedral : 4.475 19.832 1665 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.49 % Allowed : 20.28 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1522 helix: 0.80 (0.21), residues: 654 sheet: -2.26 (0.38), residues: 172 loop : -1.81 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.014 0.001 TYR A 834 PHE 0.047 0.002 PHE B 661 TRP 0.005 0.001 TRP B 713 HIS 0.002 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00331 (12202) covalent geometry : angle 0.64266 (16581) SS BOND : bond 0.00182 ( 14) SS BOND : angle 0.61255 ( 28) hydrogen bonds : bond 0.04504 ( 476) hydrogen bonds : angle 4.49099 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 105 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8101 (t) REVERT: A 287 ILE cc_start: 0.8611 (mm) cc_final: 0.8265 (mt) REVERT: A 427 TYR cc_start: 0.8296 (t80) cc_final: 0.7795 (t80) REVERT: A 654 PHE cc_start: 0.8585 (m-80) cc_final: 0.8207 (m-80) REVERT: A 695 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8228 (pp30) REVERT: A 787 MET cc_start: 0.9466 (mmm) cc_final: 0.8979 (tmm) REVERT: A 832 MET cc_start: 0.3801 (mmt) cc_final: 0.2948 (ttm) REVERT: B 76 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 105 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8092 (t) REVERT: B 113 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8765 (mm) REVERT: B 287 ILE cc_start: 0.8599 (mm) cc_final: 0.8273 (mt) REVERT: B 434 MET cc_start: 0.8139 (ttm) cc_final: 0.7638 (mtt) REVERT: B 654 PHE cc_start: 0.8439 (m-10) cc_final: 0.8078 (m-80) REVERT: B 787 MET cc_start: 0.9527 (mmm) cc_final: 0.9118 (ptm) REVERT: B 788 TYR cc_start: 0.8910 (m-10) cc_final: 0.8686 (m-80) REVERT: B 832 MET cc_start: 0.4504 (mmt) cc_final: 0.3968 (ttm) outliers start: 32 outliers final: 22 residues processed: 107 average time/residue: 0.1032 time to fit residues: 16.6482 Evaluate side-chains 104 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 632 CYS Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 74 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 141 optimal weight: 0.0470 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** 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 = 0.4168 r_free = 0.4168 target = 0.115160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.079378 restraints weight = 39258.749| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.66 r_work: 0.3267 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12216 Z= 0.138 Angle : 0.631 10.460 16609 Z= 0.316 Chirality : 0.044 0.250 1904 Planarity : 0.004 0.047 2101 Dihedral : 4.330 20.352 1665 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.95 % Allowed : 20.20 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.23), residues: 1522 helix: 0.89 (0.21), residues: 654 sheet: -2.16 (0.39), residues: 172 loop : -1.76 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 389 TYR 0.016 0.001 TYR B 319 PHE 0.046 0.002 PHE A 661 TRP 0.005 0.001 TRP B 713 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00314 (12202) covalent geometry : angle 0.63160 (16581) SS BOND : bond 0.00184 ( 14) SS BOND : angle 0.56141 ( 28) hydrogen bonds : bond 0.04355 ( 476) hydrogen bonds : angle 4.38390 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8431 (mp) REVERT: A 105 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8257 (p) REVERT: A 113 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8652 (mm) REVERT: A 287 ILE cc_start: 0.8614 (mm) cc_final: 0.8283 (mt) REVERT: A 355 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7745 (mtm180) REVERT: A 427 TYR cc_start: 0.8378 (t80) cc_final: 0.7790 (t80) REVERT: A 434 MET cc_start: 0.7790 (ttm) cc_final: 0.7417 (mtt) REVERT: A 635 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8587 (pt) REVERT: A 654 PHE cc_start: 0.8613 (m-80) cc_final: 0.8136 (m-80) REVERT: A 695 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8326 (pp30) REVERT: A 785 PHE cc_start: 0.8980 (m-10) cc_final: 0.8688 (m-80) REVERT: A 787 MET cc_start: 0.9482 (mmm) cc_final: 0.8922 (tmm) REVERT: A 822 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.9266 (ttt) REVERT: B 76 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8432 (mp) REVERT: B 113 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8754 (mm) REVERT: B 287 ILE cc_start: 0.8615 (mm) cc_final: 0.8297 (mt) REVERT: B 355 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7772 (mtm180) REVERT: B 434 MET cc_start: 0.8047 (ttm) cc_final: 0.7598 (mtt) REVERT: B 635 ILE cc_start: 0.8367 (mm) cc_final: 0.7999 (mm) REVERT: B 654 PHE cc_start: 0.8405 (m-10) cc_final: 0.8074 (m-80) REVERT: B 659 MET cc_start: 0.8054 (tmm) cc_final: 0.7709 (ppp) REVERT: B 787 MET cc_start: 0.9503 (mmm) cc_final: 0.8896 (tmm) REVERT: B 832 MET cc_start: 0.4672 (mmt) cc_final: 0.3989 (ttp) outliers start: 38 outliers final: 18 residues processed: 110 average time/residue: 0.1096 time to fit residues: 17.9631 Evaluate side-chains 103 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** 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 = 0.4183 r_free = 0.4183 target = 0.115745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080224 restraints weight = 39461.525| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.66 r_work: 0.3279 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12216 Z= 0.123 Angle : 0.633 10.614 16609 Z= 0.313 Chirality : 0.045 0.238 1904 Planarity : 0.004 0.047 2101 Dihedral : 4.218 20.581 1665 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.56 % Allowed : 20.51 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1522 helix: 0.99 (0.21), residues: 654 sheet: -2.10 (0.39), residues: 172 loop : -1.72 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 389 TYR 0.015 0.001 TYR A 834 PHE 0.049 0.002 PHE A 661 TRP 0.004 0.001 TRP B 583 HIS 0.002 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00277 (12202) covalent geometry : angle 0.63313 (16581) SS BOND : bond 0.00176 ( 14) SS BOND : angle 0.53573 ( 28) hydrogen bonds : bond 0.04176 ( 476) hydrogen bonds : angle 4.29319 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 287 ILE cc_start: 0.8610 (mm) cc_final: 0.8281 (mt) REVERT: A 355 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7740 (mtm180) REVERT: A 427 TYR cc_start: 0.8228 (t80) cc_final: 0.7895 (t80) REVERT: A 434 MET cc_start: 0.7859 (ttm) cc_final: 0.7363 (mtp) REVERT: A 654 PHE cc_start: 0.8566 (m-80) cc_final: 0.8210 (m-80) REVERT: A 695 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8146 (pp30) REVERT: A 785 PHE cc_start: 0.8978 (m-10) cc_final: 0.8673 (m-80) REVERT: A 787 MET cc_start: 0.9484 (mmm) cc_final: 0.8925 (tmm) REVERT: B 48 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8545 (pp) REVERT: B 76 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8391 (mp) REVERT: B 113 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8717 (mm) REVERT: B 287 ILE cc_start: 0.8600 (mm) cc_final: 0.8285 (mt) REVERT: B 355 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7757 (mtm180) REVERT: B 635 ILE cc_start: 0.8310 (mm) cc_final: 0.8007 (mm) REVERT: B 654 PHE cc_start: 0.8441 (m-10) cc_final: 0.8098 (m-80) REVERT: B 659 MET cc_start: 0.7947 (tmm) cc_final: 0.7647 (ppp) REVERT: B 787 MET cc_start: 0.9432 (mmm) cc_final: 0.8864 (tmm) REVERT: B 832 MET cc_start: 0.4908 (mmt) cc_final: 0.3911 (ttp) outliers start: 33 outliers final: 20 residues processed: 109 average time/residue: 0.1040 time to fit residues: 16.5546 Evaluate side-chains 106 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 29 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** 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 = 0.4177 r_free = 0.4177 target = 0.118633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084513 restraints weight = 40956.033| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.58 r_work: 0.3291 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12216 Z= 0.129 Angle : 0.628 10.306 16609 Z= 0.312 Chirality : 0.045 0.240 1904 Planarity : 0.004 0.046 2101 Dihedral : 4.149 20.308 1665 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.41 % Allowed : 20.67 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.23), residues: 1522 helix: 1.00 (0.21), residues: 656 sheet: -2.04 (0.39), residues: 172 loop : -1.70 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 240 TYR 0.017 0.001 TYR B 319 PHE 0.047 0.002 PHE B 661 TRP 0.004 0.001 TRP A 583 HIS 0.002 0.000 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00296 (12202) covalent geometry : angle 0.62855 (16581) SS BOND : bond 0.00175 ( 14) SS BOND : angle 0.49866 ( 28) hydrogen bonds : bond 0.04175 ( 476) hydrogen bonds : angle 4.28097 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 113 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8589 (mm) REVERT: A 287 ILE cc_start: 0.8617 (mm) cc_final: 0.8305 (mt) REVERT: A 355 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7733 (mtm180) REVERT: A 427 TYR cc_start: 0.8326 (t80) cc_final: 0.7935 (t80) REVERT: A 434 MET cc_start: 0.7667 (ttm) cc_final: 0.7416 (mtp) REVERT: A 654 PHE cc_start: 0.8547 (m-80) cc_final: 0.8257 (m-80) REVERT: A 695 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8125 (pp30) REVERT: A 785 PHE cc_start: 0.9065 (m-10) cc_final: 0.8801 (m-80) REVERT: A 787 MET cc_start: 0.9487 (mmm) cc_final: 0.8925 (tmm) REVERT: B 48 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8544 (pp) REVERT: B 76 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8422 (mp) REVERT: B 113 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8679 (mm) REVERT: B 287 ILE cc_start: 0.8617 (mm) cc_final: 0.8316 (mt) REVERT: B 355 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7763 (mtm180) REVERT: B 635 ILE cc_start: 0.8437 (mm) cc_final: 0.8199 (mm) REVERT: B 654 PHE cc_start: 0.8443 (m-10) cc_final: 0.8062 (m-80) REVERT: B 659 MET cc_start: 0.7914 (tmm) cc_final: 0.7588 (ppp) REVERT: B 787 MET cc_start: 0.9428 (mmm) cc_final: 0.8836 (tmm) REVERT: B 832 MET cc_start: 0.5364 (mmt) cc_final: 0.4536 (ttm) outliers start: 31 outliers final: 23 residues processed: 112 average time/residue: 0.1044 time to fit residues: 16.9688 Evaluate side-chains 110 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 569 CYS Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 11 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 139 optimal weight: 0.0970 chunk 124 optimal weight: 0.8980 chunk 140 optimal weight: 0.0020 chunk 19 optimal weight: 0.0670 chunk 115 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 overall best weight: 0.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 398 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 = 0.4209 r_free = 0.4209 target = 0.120607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087659 restraints weight = 41546.636| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.82 r_work: 0.3324 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12216 Z= 0.112 Angle : 0.647 11.077 16609 Z= 0.317 Chirality : 0.044 0.199 1904 Planarity : 0.004 0.070 2101 Dihedral : 4.101 20.241 1665 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.40 % Allowed : 22.46 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1522 helix: 1.05 (0.21), residues: 656 sheet: -1.88 (0.40), residues: 168 loop : -1.71 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 240 TYR 0.015 0.001 TYR A 834 PHE 0.049 0.001 PHE A 661 TRP 0.005 0.001 TRP A 358 HIS 0.001 0.000 HIS B 537 Details of bonding type rmsd covalent geometry : bond 0.00247 (12202) covalent geometry : angle 0.64750 (16581) SS BOND : bond 0.00194 ( 14) SS BOND : angle 0.49116 ( 28) hydrogen bonds : bond 0.03832 ( 476) hydrogen bonds : angle 4.19464 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8423 (pp) REVERT: A 113 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8721 (mm) REVERT: A 269 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7065 (mm) REVERT: A 287 ILE cc_start: 0.8608 (mm) cc_final: 0.8318 (mt) REVERT: A 427 TYR cc_start: 0.8288 (t80) cc_final: 0.7911 (t80) REVERT: A 434 MET cc_start: 0.7981 (ttm) cc_final: 0.7345 (mtt) REVERT: A 654 PHE cc_start: 0.8496 (m-80) cc_final: 0.8128 (m-80) REVERT: A 695 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8221 (pp30) REVERT: A 785 PHE cc_start: 0.9088 (m-10) cc_final: 0.8806 (m-80) REVERT: A 787 MET cc_start: 0.9487 (mmm) cc_final: 0.8914 (tmm) REVERT: B 48 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8470 (pp) REVERT: B 113 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8612 (mm) REVERT: B 269 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.6987 (mm) REVERT: B 287 ILE cc_start: 0.8600 (mm) cc_final: 0.8317 (mt) REVERT: B 635 ILE cc_start: 0.8442 (mm) cc_final: 0.8161 (mm) REVERT: B 654 PHE cc_start: 0.8258 (m-10) cc_final: 0.7867 (m-80) REVERT: B 659 MET cc_start: 0.7818 (tmm) cc_final: 0.7476 (ppp) REVERT: B 787 MET cc_start: 0.9418 (mmm) cc_final: 0.9097 (ptm) REVERT: B 832 MET cc_start: 0.4824 (mmt) cc_final: 0.3888 (ttp) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 0.0955 time to fit residues: 13.8279 Evaluate side-chains 89 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 579 TRP Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 579 TRP Chi-restraints excluded: chain B residue 637 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 19 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.121576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.089740 restraints weight = 39797.059| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.66 r_work: 0.3286 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12216 Z= 0.127 Angle : 0.637 10.260 16609 Z= 0.315 Chirality : 0.044 0.176 1904 Planarity : 0.004 0.046 2101 Dihedral : 4.046 19.986 1665 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.63 % Allowed : 21.99 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1522 helix: 1.13 (0.21), residues: 654 sheet: -1.89 (0.40), residues: 168 loop : -1.67 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 240 TYR 0.017 0.001 TYR B 319 PHE 0.050 0.002 PHE A 661 TRP 0.003 0.001 TRP B 583 HIS 0.002 0.000 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00292 (12202) covalent geometry : angle 0.63729 (16581) SS BOND : bond 0.00171 ( 14) SS BOND : angle 0.47104 ( 28) hydrogen bonds : bond 0.04002 ( 476) hydrogen bonds : angle 4.25047 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.01 seconds wall clock time: 57 minutes 15.01 seconds (3435.01 seconds total)