Starting phenix.real_space_refine on Thu Nov 20 14:03:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djb_7935/11_2025/6djb_7935.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djb_7935/11_2025/6djb_7935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6djb_7935/11_2025/6djb_7935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djb_7935/11_2025/6djb_7935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6djb_7935/11_2025/6djb_7935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djb_7935/11_2025/6djb_7935.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 22569 2.51 5 N 5889 2.21 5 O 6099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34707 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5739 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 27, 'TRANS': 678} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 5830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5830 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 27, 'TRANS': 697} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 92 Restraints were copied for chains: E, C, F, D Time building chain proxies: 10.91, per 1000 atoms: 0.31 Number of scatterers: 34707 At special positions: 0 Unit cell: (144.9, 146.05, 187.45, 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 150 16.00 O 6099 8.00 N 5889 7.00 C 22569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.02 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.02 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.01 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.02 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.02 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.02 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.01 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.01 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 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: 3.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8334 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 15 sheets defined 48.2% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 24 through 50 removed outlier: 3.979A pdb=" N ASP A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 removed outlier: 3.580A pdb=" N TYR A 124 " --> pdb=" O TRP A 120 " (cutoff:3.500A) Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.506A pdb=" N THR A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.989A pdb=" N GLU A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 285 removed outlier: 3.679A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 314 through 345 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.217A pdb=" N SER A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.652A pdb=" N LEU A 445 " --> pdb=" O VAL A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.579A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 703 through 707 Processing helix chain 'A' and resid 724 through 729 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 770 through 775 removed outlier: 3.679A pdb=" N LEU A 773 " --> pdb=" O PRO A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 25 through 49 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.546A pdb=" N ASN B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 140 Processing helix chain 'B' and resid 146 through 164 removed outlier: 5.358A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.630A pdb=" N VAL B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 Processing helix chain 'B' and resid 258 through 285 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 313 through 346 removed outlier: 4.470A pdb=" N LEU B 317 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 370 through 381 removed outlier: 3.788A pdb=" N GLN B 381 " --> pdb=" O HIS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 394 removed outlier: 4.094A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 411 Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 528 through 540 Processing helix chain 'B' and resid 559 through 566 removed outlier: 4.008A pdb=" N THR B 563 " --> pdb=" O PRO B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 591 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 657 through 661 Processing helix chain 'B' and resid 680 through 684 Processing helix chain 'B' and resid 701 through 706 removed outlier: 4.025A pdb=" N ILE B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.783A pdb=" N THR B 754 " --> pdb=" O GLY B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 776 Processing helix chain 'B' and resid 794 through 802 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 50 removed outlier: 3.979A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 141 removed outlier: 3.580A pdb=" N TYR E 124 " --> pdb=" O TRP E 120 " (cutoff:3.500A) Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 149 through 165 Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.506A pdb=" N THR E 170 " --> pdb=" O SER E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.989A pdb=" N GLU E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 285 removed outlier: 3.679A pdb=" N ARG E 262 " --> pdb=" O ASP E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 314 through 345 Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 370 through 383 Processing helix chain 'E' and resid 383 through 394 removed outlier: 4.218A pdb=" N SER E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 411 Processing helix chain 'E' and resid 412 through 419 Processing helix chain 'E' and resid 439 through 445 removed outlier: 3.652A pdb=" N LEU E 445 " --> pdb=" O VAL E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 468 Processing helix chain 'E' and resid 487 through 494 Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.579A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 586 through 591 Processing helix chain 'E' and resid 634 through 638 Processing helix chain 'E' and resid 656 through 661 Processing helix chain 'E' and resid 703 through 707 Processing helix chain 'E' and resid 724 through 729 Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 770 through 775 removed outlier: 3.679A pdb=" N LEU E 773 " --> pdb=" O PRO E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 794 through 802 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 25 through 49 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.547A pdb=" N ASN F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 124 through 140 Processing helix chain 'F' and resid 146 through 164 removed outlier: 5.358A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE F 164 " --> pdb=" O LEU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 Processing helix chain 'F' and resid 220 through 227 removed outlier: 3.629A pdb=" N VAL F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 255 Processing helix chain 'F' and resid 258 through 285 Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 313 through 346 removed outlier: 4.470A pdb=" N LEU F 317 " --> pdb=" O PRO F 313 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG F 346 " --> pdb=" O TRP F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 370 through 381 removed outlier: 3.788A pdb=" N GLN F 381 " --> pdb=" O HIS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 394 removed outlier: 4.095A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 411 Processing helix chain 'F' and resid 412 through 417 Processing helix chain 'F' and resid 418 through 420 No H-bonds generated for 'chain 'F' and resid 418 through 420' Processing helix chain 'F' and resid 440 through 445 Processing helix chain 'F' and resid 487 through 492 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 528 through 540 Processing helix chain 'F' and resid 559 through 566 removed outlier: 4.009A pdb=" N THR F 563 " --> pdb=" O PRO F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 591 Processing helix chain 'F' and resid 607 through 613 Processing helix chain 'F' and resid 634 through 638 Processing helix chain 'F' and resid 657 through 661 Processing helix chain 'F' and resid 680 through 684 Processing helix chain 'F' and resid 701 through 706 removed outlier: 4.025A pdb=" N ILE F 704 " --> pdb=" O PRO F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 729 Processing helix chain 'F' and resid 747 through 754 removed outlier: 3.783A pdb=" N THR F 754 " --> pdb=" O GLY F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 776 Processing helix chain 'F' and resid 794 through 802 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 24 through 50 removed outlier: 3.979A pdb=" N ASP C 50 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 117 Processing helix chain 'C' and resid 119 through 141 removed outlier: 3.581A pdb=" N TYR C 124 " --> pdb=" O TRP C 120 " (cutoff:3.500A) Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 149 through 165 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.507A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 256 removed outlier: 3.989A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 285 removed outlier: 3.679A pdb=" N ARG C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 314 through 345 Processing helix chain 'C' and resid 353 through 358 Processing helix chain 'C' and resid 370 through 383 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.217A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 411 Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 439 through 445 removed outlier: 3.652A pdb=" N LEU C 445 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 487 through 494 Processing helix chain 'C' and resid 528 through 541 Processing helix chain 'C' and resid 559 through 566 removed outlier: 3.579A pdb=" N THR C 563 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 586 through 591 Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 703 through 707 Processing helix chain 'C' and resid 724 through 729 Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 770 through 775 removed outlier: 3.679A pdb=" N LEU C 773 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 802 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 25 through 49 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.545A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 124 through 140 Processing helix chain 'D' and resid 146 through 164 removed outlier: 5.358A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 220 through 227 removed outlier: 3.630A pdb=" N VAL D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 255 Processing helix chain 'D' and resid 258 through 285 Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 313 through 346 removed outlier: 4.470A pdb=" N LEU D 317 " --> pdb=" O PRO D 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 370 through 381 removed outlier: 3.788A pdb=" N GLN D 381 " --> pdb=" O HIS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 394 removed outlier: 4.095A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 411 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 418 through 420 No H-bonds generated for 'chain 'D' and resid 418 through 420' Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 528 through 540 Processing helix chain 'D' and resid 559 through 566 removed outlier: 4.008A pdb=" N THR D 563 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 591 Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'D' and resid 657 through 661 Processing helix chain 'D' and resid 680 through 684 Processing helix chain 'D' and resid 701 through 706 removed outlier: 4.026A pdb=" N ILE D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 729 Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.784A pdb=" N THR D 754 " --> pdb=" O GLY D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 776 Processing helix chain 'D' and resid 794 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 421 removed outlier: 6.379A pdb=" N LEU A 430 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 432 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 451 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR A 642 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 667 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU A 644 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU A 669 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A 689 " --> pdb=" O GLU A 665 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 352 removed outlier: 3.686A pdb=" N TYR B 351 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B 368 " --> pdb=" O TYR B 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.556A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR B 642 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 667 " --> pdb=" O THR B 642 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 644 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 669 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR B 689 " --> pdb=" O GLU B 665 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG B 762 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 738 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AA7, first strand: chain 'E' and resid 420 through 421 removed outlier: 6.379A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 451 " --> pdb=" O GLU E 473 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR E 642 " --> pdb=" O GLU E 665 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU E 667 " --> pdb=" O THR E 642 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU E 644 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU E 669 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR E 689 " --> pdb=" O GLU E 665 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=AA9, first strand: chain 'F' and resid 350 through 352 removed outlier: 3.686A pdb=" N TYR F 351 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL F 368 " --> pdb=" O TYR F 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 431 through 432 removed outlier: 3.555A pdb=" N ILE F 619 " --> pdb=" O CYS F 643 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR F 642 " --> pdb=" O GLU F 665 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU F 667 " --> pdb=" O THR F 642 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU F 644 " --> pdb=" O LEU F 667 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU F 669 " --> pdb=" O LEU F 644 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR F 689 " --> pdb=" O GLU F 665 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU F 736 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG F 762 " --> pdb=" O LEU F 736 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU F 738 " --> pdb=" O ARG F 762 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB3, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.378A pdb=" N LEU C 430 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU C 454 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU C 432 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 451 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR C 642 " --> pdb=" O GLU C 665 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU C 667 " --> pdb=" O THR C 642 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU C 644 " --> pdb=" O LEU C 667 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU C 669 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR C 689 " --> pdb=" O GLU C 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 352 removed outlier: 3.687A pdb=" N TYR D 351 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D 368 " --> pdb=" O TYR D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 431 through 432 removed outlier: 3.556A pdb=" N ILE D 619 " --> pdb=" O CYS D 643 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR D 642 " --> pdb=" O GLU D 665 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D 667 " --> pdb=" O THR D 642 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU D 644 " --> pdb=" O LEU D 667 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU D 669 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR D 689 " --> pdb=" O GLU D 665 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU D 736 " --> pdb=" O GLU D 760 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ARG D 762 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU D 738 " --> pdb=" O ARG D 762 " (cutoff:3.500A) 1644 hydrogen bonds defined for protein. 4401 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: 7.65 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8361 1.33 - 1.46: 9004 1.46 - 1.58: 17894 1.58 - 1.71: 3 1.71 - 1.84: 201 Bond restraints: 35463 Sorted by residual: bond pdb=" CB ILE F 629 " pdb=" CG2 ILE F 629 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.46e+01 bond pdb=" CB ILE B 629 " pdb=" CG2 ILE B 629 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.45e+01 bond pdb=" CB ILE D 629 " pdb=" CG2 ILE D 629 " ideal model delta sigma weight residual 1.521 1.395 0.126 3.30e-02 9.18e+02 1.45e+01 bond pdb=" CB CYS F 310 " pdb=" SG CYS F 310 " ideal model delta sigma weight residual 1.808 1.684 0.124 3.30e-02 9.18e+02 1.42e+01 bond pdb=" CB CYS B 310 " pdb=" SG CYS B 310 " ideal model delta sigma weight residual 1.808 1.684 0.124 3.30e-02 9.18e+02 1.42e+01 ... (remaining 35458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 40342 2.00 - 4.00: 6330 4.00 - 6.00: 1116 6.00 - 8.00: 269 8.00 - 10.01: 51 Bond angle restraints: 48108 Sorted by residual: angle pdb=" N SER E 464 " pdb=" CA SER E 464 " pdb=" C SER E 464 " ideal model delta sigma weight residual 112.54 102.53 10.01 1.51e+00 4.39e-01 4.39e+01 angle pdb=" N SER A 464 " pdb=" CA SER A 464 " pdb=" C SER A 464 " ideal model delta sigma weight residual 112.54 102.56 9.98 1.51e+00 4.39e-01 4.37e+01 angle pdb=" N SER C 464 " pdb=" CA SER C 464 " pdb=" C SER C 464 " ideal model delta sigma weight residual 112.54 102.58 9.96 1.51e+00 4.39e-01 4.35e+01 angle pdb=" C ILE B 654 " pdb=" N PRO B 655 " pdb=" CA PRO B 655 " ideal model delta sigma weight residual 119.84 127.51 -7.67 1.25e+00 6.40e-01 3.76e+01 angle pdb=" C ILE F 654 " pdb=" N PRO F 655 " pdb=" CA PRO F 655 " ideal model delta sigma weight residual 119.84 127.49 -7.65 1.25e+00 6.40e-01 3.75e+01 ... (remaining 48103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 20608 16.11 - 32.21: 710 32.21 - 48.32: 66 48.32 - 64.42: 72 64.42 - 80.53: 6 Dihedral angle restraints: 21462 sinusoidal: 8685 harmonic: 12777 Sorted by residual: dihedral pdb=" N LEU F 432 " pdb=" C LEU F 432 " pdb=" CA LEU F 432 " pdb=" CB LEU F 432 " ideal model delta harmonic sigma weight residual 122.80 111.49 11.31 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" N LEU B 432 " pdb=" C LEU B 432 " pdb=" CA LEU B 432 " pdb=" CB LEU B 432 " ideal model delta harmonic sigma weight residual 122.80 111.51 11.29 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" N LEU D 432 " pdb=" C LEU D 432 " pdb=" CA LEU D 432 " pdb=" CB LEU D 432 " ideal model delta harmonic sigma weight residual 122.80 111.52 11.28 0 2.50e+00 1.60e-01 2.04e+01 ... (remaining 21459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4338 0.081 - 0.163: 1064 0.163 - 0.244: 184 0.244 - 0.326: 18 0.326 - 0.407: 12 Chirality restraints: 5616 Sorted by residual: chirality pdb=" CB ILE F 629 " pdb=" CA ILE F 629 " pdb=" CG1 ILE F 629 " pdb=" CG2 ILE F 629 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CB ILE B 629 " pdb=" CA ILE B 629 " pdb=" CG1 ILE B 629 " pdb=" CG2 ILE B 629 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CB ILE D 629 " pdb=" CA ILE D 629 " pdb=" CG1 ILE D 629 " pdb=" CG2 ILE D 629 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 5613 not shown) Planarity restraints: 5961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 513 " 0.015 2.00e-02 2.50e+03 4.59e-02 4.20e+01 pdb=" CG TYR F 513 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR F 513 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR F 513 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR F 513 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR F 513 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR F 513 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 513 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 513 " 0.015 2.00e-02 2.50e+03 4.58e-02 4.19e+01 pdb=" CG TYR D 513 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR D 513 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 513 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR D 513 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 513 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR D 513 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 513 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 513 " -0.015 2.00e-02 2.50e+03 4.57e-02 4.19e+01 pdb=" CG TYR B 513 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR B 513 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR B 513 " 0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR B 513 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 513 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 513 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 513 " -0.022 2.00e-02 2.50e+03 ... (remaining 5958 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 12797 2.88 - 3.39: 34341 3.39 - 3.89: 59480 3.89 - 4.40: 68776 4.40 - 4.90: 109204 Nonbonded interactions: 284598 Sorted by model distance: nonbonded pdb=" NZ LYS E 98 " pdb=" OD2 ASP D 100 " model vdw 2.377 3.120 nonbonded pdb=" NZ LYS A 98 " pdb=" OD2 ASP F 100 " model vdw 2.377 3.120 nonbonded pdb=" OD2 ASP B 100 " pdb=" NZ LYS C 98 " model vdw 2.377 3.120 nonbonded pdb=" NZ LYS B 580 " pdb=" OD2 ASP B 602 " model vdw 2.398 3.120 nonbonded pdb=" NZ LYS F 580 " pdb=" OD2 ASP F 602 " model vdw 2.398 3.120 ... (remaining 284593 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 35.820 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.013 0.140 35481 Z= 0.618 Angle : 1.592 10.006 48144 Z= 0.996 Chirality : 0.074 0.407 5616 Planarity : 0.010 0.065 5961 Dihedral : 9.158 80.525 13074 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.40 % Favored : 92.39 % Rotamer: Outliers : 0.08 % Allowed : 1.03 % Favored : 98.89 % Cbeta Deviations : 0.07 % 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: -1.85 (0.13), residues: 4257 helix: -0.40 (0.12), residues: 1830 sheet: -1.78 (0.21), residues: 597 loop : -1.81 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 765 TYR 0.096 0.015 TYR C 127 PHE 0.090 0.013 PHE B 443 TRP 0.065 0.008 TRP C 647 HIS 0.021 0.004 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.01296 (35463) covalent geometry : angle 1.59027 (48108) SS BOND : bond 0.01249 ( 18) SS BOND : angle 2.84468 ( 36) hydrogen bonds : bond 0.17750 ( 1644) hydrogen bonds : angle 7.30529 ( 4401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1135 time to evaluate : 1.219 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: 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: 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 35 MET cc_start: 0.9346 (mtp) cc_final: 0.8873 (mtm) REVERT: A 99 TYR cc_start: 0.7503 (m-80) cc_final: 0.7224 (m-80) REVERT: A 151 SER cc_start: 0.8582 (p) cc_final: 0.8136 (m) REVERT: A 261 TYR cc_start: 0.8897 (t80) cc_final: 0.8509 (t80) REVERT: A 299 ILE cc_start: 0.9198 (pt) cc_final: 0.8944 (pt) REVERT: A 434 MET cc_start: 0.7979 (mmm) cc_final: 0.7531 (mmm) REVERT: A 454 GLU cc_start: 0.8409 (pt0) cc_final: 0.6260 (pt0) REVERT: A 461 ILE cc_start: 0.8757 (mm) cc_final: 0.8447 (mm) REVERT: A 518 LEU cc_start: 0.7113 (mt) cc_final: 0.6892 (mt) REVERT: A 641 LEU cc_start: 0.9326 (tp) cc_final: 0.8869 (tt) REVERT: A 665 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7751 (mp0) REVERT: A 748 SER cc_start: 0.8563 (p) cc_final: 0.8084 (m) REVERT: B 35 MET cc_start: 0.8915 (mtt) cc_final: 0.8592 (ttm) REVERT: B 38 ILE cc_start: 0.9552 (tt) cc_final: 0.9279 (mm) REVERT: B 241 LYS cc_start: 0.9572 (tttt) cc_final: 0.9359 (tptp) REVERT: B 343 MET cc_start: 0.8415 (mtp) cc_final: 0.8103 (mtp) REVERT: B 402 LEU cc_start: 0.9429 (tp) cc_final: 0.9099 (tp) REVERT: B 440 ASP cc_start: 0.8489 (m-30) cc_final: 0.8182 (m-30) REVERT: B 476 LEU cc_start: 0.9146 (mt) cc_final: 0.8880 (tt) REVERT: B 491 LEU cc_start: 0.9441 (mt) cc_final: 0.9128 (tp) REVERT: B 519 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7688 (mm-30) REVERT: B 540 LEU cc_start: 0.8719 (mt) cc_final: 0.8345 (tt) REVERT: B 546 LEU cc_start: 0.9504 (tp) cc_final: 0.9161 (tp) REVERT: B 629 ILE cc_start: 0.8982 (tt) cc_final: 0.8776 (tt) REVERT: B 692 LEU cc_start: 0.9208 (mt) cc_final: 0.8895 (pp) REVERT: B 733 LEU cc_start: 0.8065 (tp) cc_final: 0.7659 (tp) REVERT: B 782 SER cc_start: 0.9292 (t) cc_final: 0.9073 (p) REVERT: E 35 MET cc_start: 0.9404 (mtp) cc_final: 0.8937 (mtm) REVERT: E 51 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8845 (mtmt) REVERT: E 52 MET cc_start: 0.8298 (mmm) cc_final: 0.7724 (mmm) REVERT: E 99 TYR cc_start: 0.7435 (m-80) cc_final: 0.6892 (m-80) REVERT: E 110 ASP cc_start: 0.9204 (m-30) cc_final: 0.8894 (t0) REVERT: E 151 SER cc_start: 0.8502 (p) cc_final: 0.8123 (m) REVERT: E 261 TYR cc_start: 0.8954 (t80) cc_final: 0.8442 (t80) REVERT: E 299 ILE cc_start: 0.9216 (pt) cc_final: 0.8919 (pt) REVERT: E 326 ILE cc_start: 0.9574 (mt) cc_final: 0.9239 (tp) REVERT: E 380 ASP cc_start: 0.8185 (t70) cc_final: 0.7796 (t0) REVERT: E 434 MET cc_start: 0.7594 (mmm) cc_final: 0.6749 (mmm) REVERT: E 454 GLU cc_start: 0.8546 (pt0) cc_final: 0.6323 (pt0) REVERT: E 461 ILE cc_start: 0.8564 (mm) cc_final: 0.8274 (mm) REVERT: E 518 LEU cc_start: 0.7222 (mt) cc_final: 0.6820 (mt) REVERT: E 641 LEU cc_start: 0.9317 (tp) cc_final: 0.8926 (tt) REVERT: F 35 MET cc_start: 0.8911 (mtt) cc_final: 0.8408 (ttm) REVERT: F 51 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8804 (mmmt) REVERT: F 52 MET cc_start: 0.8003 (tpp) cc_final: 0.7437 (tpp) REVERT: F 129 VAL cc_start: 0.9010 (t) cc_final: 0.8765 (p) REVERT: F 337 MET cc_start: 0.8786 (mmm) cc_final: 0.8530 (ppp) REVERT: F 343 MET cc_start: 0.8569 (mtp) cc_final: 0.8298 (mtp) REVERT: F 402 LEU cc_start: 0.9438 (tp) cc_final: 0.9114 (tp) REVERT: F 414 ASP cc_start: 0.8609 (m-30) cc_final: 0.8361 (m-30) REVERT: F 428 LEU cc_start: 0.7988 (mt) cc_final: 0.7588 (mm) REVERT: F 440 ASP cc_start: 0.8622 (m-30) cc_final: 0.8278 (m-30) REVERT: F 471 LEU cc_start: 0.9256 (tp) cc_final: 0.9018 (tt) REVERT: F 491 LEU cc_start: 0.9443 (mt) cc_final: 0.9114 (tp) REVERT: F 540 LEU cc_start: 0.8656 (mt) cc_final: 0.8287 (tt) REVERT: F 629 ILE cc_start: 0.8979 (tt) cc_final: 0.8759 (tt) REVERT: F 676 LYS cc_start: 0.8121 (pttt) cc_final: 0.7862 (tppt) REVERT: F 692 LEU cc_start: 0.9269 (mt) cc_final: 0.8848 (pp) REVERT: F 744 GLN cc_start: 0.8215 (mp10) cc_final: 0.7960 (pp30) REVERT: C 35 MET cc_start: 0.9333 (mtp) cc_final: 0.8821 (mtm) REVERT: C 52 MET cc_start: 0.8594 (mmm) cc_final: 0.7866 (mmm) REVERT: C 99 TYR cc_start: 0.7629 (m-80) cc_final: 0.7076 (m-80) REVERT: C 110 ASP cc_start: 0.9239 (m-30) cc_final: 0.8979 (t70) REVERT: C 129 VAL cc_start: 0.9187 (t) cc_final: 0.8803 (p) REVERT: C 151 SER cc_start: 0.8485 (p) cc_final: 0.7987 (m) REVERT: C 164 PHE cc_start: 0.8484 (t80) cc_final: 0.8169 (t80) REVERT: C 238 GLU cc_start: 0.8920 (tt0) cc_final: 0.8698 (mp0) REVERT: C 261 TYR cc_start: 0.8900 (t80) cc_final: 0.8344 (t80) REVERT: C 434 MET cc_start: 0.7774 (mmm) cc_final: 0.6647 (mmm) REVERT: C 454 GLU cc_start: 0.8574 (pt0) cc_final: 0.7072 (pt0) REVERT: C 461 ILE cc_start: 0.8560 (mm) cc_final: 0.8237 (mm) REVERT: C 518 LEU cc_start: 0.7125 (mt) cc_final: 0.6739 (mt) REVERT: C 620 ASP cc_start: 0.7933 (t0) cc_final: 0.7695 (p0) REVERT: C 641 LEU cc_start: 0.9344 (tp) cc_final: 0.9112 (tp) REVERT: D 28 THR cc_start: 0.9326 (m) cc_final: 0.9088 (p) REVERT: D 35 MET cc_start: 0.8964 (mtt) cc_final: 0.8394 (ttm) REVERT: D 38 ILE cc_start: 0.9512 (tt) cc_final: 0.9143 (mm) REVERT: D 129 VAL cc_start: 0.9156 (t) cc_final: 0.8705 (p) REVERT: D 239 GLN cc_start: 0.8916 (mt0) cc_final: 0.8441 (tt0) REVERT: D 308 TYR cc_start: 0.8744 (m-80) cc_final: 0.8516 (m-80) REVERT: D 325 TYR cc_start: 0.8967 (t80) cc_final: 0.8604 (t80) REVERT: D 337 MET cc_start: 0.8646 (mmm) cc_final: 0.8408 (ppp) REVERT: D 343 MET cc_start: 0.8722 (mtp) cc_final: 0.8427 (mtp) REVERT: D 402 LEU cc_start: 0.9443 (tp) cc_final: 0.9177 (tp) REVERT: D 432 LEU cc_start: 0.8919 (mt) cc_final: 0.8687 (mt) REVERT: D 438 ILE cc_start: 0.8618 (mm) cc_final: 0.8375 (pt) REVERT: D 440 ASP cc_start: 0.8511 (m-30) cc_final: 0.8247 (m-30) REVERT: D 491 LEU cc_start: 0.9415 (mt) cc_final: 0.9082 (tp) REVERT: D 540 LEU cc_start: 0.8559 (mt) cc_final: 0.8236 (tt) REVERT: D 629 ILE cc_start: 0.8935 (tt) cc_final: 0.8723 (tt) REVERT: D 676 LYS cc_start: 0.8119 (pttt) cc_final: 0.7856 (tppt) REVERT: D 692 LEU cc_start: 0.9231 (mt) cc_final: 0.8851 (pp) outliers start: 3 outliers final: 0 residues processed: 1138 average time/residue: 0.2360 time to fit residues: 420.0668 Evaluate side-chains 548 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN A 737 HIS ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS E 119 HIS E 625 ASN E 737 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 HIS C 418 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN D 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.064627 restraints weight = 158525.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.066804 restraints weight = 84394.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068255 restraints weight = 52811.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069253 restraints weight = 37033.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069930 restraints weight = 28309.931| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35481 Z= 0.185 Angle : 0.809 9.416 48144 Z= 0.438 Chirality : 0.049 0.344 5616 Planarity : 0.005 0.059 5961 Dihedral : 5.087 25.848 4659 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.73 % Favored : 92.20 % Rotamer: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 4257 helix: -0.12 (0.12), residues: 1905 sheet: -1.52 (0.21), residues: 594 loop : -2.12 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 685 TYR 0.039 0.002 TYR C 477 PHE 0.031 0.003 PHE F 393 TRP 0.029 0.002 TRP C 647 HIS 0.012 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00390 (35463) covalent geometry : angle 0.80775 (48108) SS BOND : bond 0.01433 ( 18) SS BOND : angle 1.86504 ( 36) hydrogen bonds : bond 0.06302 ( 1644) hydrogen bonds : angle 5.85975 ( 4401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 727 time to evaluate : 1.305 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: 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: A 99 TYR cc_start: 0.7034 (m-80) cc_final: 0.6749 (m-80) REVERT: A 265 MET cc_start: 0.8989 (mmt) cc_final: 0.7839 (mmm) REVERT: A 343 MET cc_start: 0.8751 (mmm) cc_final: 0.8275 (tmm) REVERT: A 434 MET cc_start: 0.7711 (mmm) cc_final: 0.7462 (mmm) REVERT: A 468 LEU cc_start: 0.8946 (mp) cc_final: 0.8566 (mt) REVERT: A 526 ASN cc_start: 0.9426 (m-40) cc_final: 0.8276 (p0) REVERT: A 623 ASP cc_start: 0.8375 (m-30) cc_final: 0.7179 (t0) REVERT: A 738 LEU cc_start: 0.9679 (mt) cc_final: 0.9303 (mp) REVERT: A 760 GLU cc_start: 0.9323 (tt0) cc_final: 0.9112 (tm-30) REVERT: A 761 LEU cc_start: 0.8988 (mp) cc_final: 0.8624 (mp) REVERT: B 132 HIS cc_start: 0.8984 (m-70) cc_final: 0.8581 (m90) REVERT: B 337 MET cc_start: 0.7785 (ppp) cc_final: 0.7531 (tmm) REVERT: B 430 LEU cc_start: 0.9003 (tt) cc_final: 0.8542 (tp) REVERT: B 473 GLU cc_start: 0.8345 (tt0) cc_final: 0.8004 (tt0) REVERT: B 491 LEU cc_start: 0.9362 (mt) cc_final: 0.8891 (tp) REVERT: B 513 TYR cc_start: 0.7531 (p90) cc_final: 0.7312 (p90) REVERT: B 519 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7801 (mm-30) REVERT: B 540 LEU cc_start: 0.8567 (mt) cc_final: 0.8180 (tt) REVERT: B 733 LEU cc_start: 0.8231 (tp) cc_final: 0.7930 (tp) REVERT: B 782 SER cc_start: 0.9343 (t) cc_final: 0.9108 (p) REVERT: E 51 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8434 (mtmt) REVERT: E 99 TYR cc_start: 0.6787 (m-80) cc_final: 0.6443 (m-80) REVERT: E 236 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8456 (mt-10) REVERT: E 261 TYR cc_start: 0.8320 (t80) cc_final: 0.7973 (t80) REVERT: E 265 MET cc_start: 0.9084 (mmt) cc_final: 0.7914 (mmm) REVERT: E 343 MET cc_start: 0.8800 (mmm) cc_final: 0.8375 (tmm) REVERT: E 433 PHE cc_start: 0.8132 (p90) cc_final: 0.7798 (p90) REVERT: E 434 MET cc_start: 0.7504 (mmm) cc_final: 0.7195 (mmm) REVERT: E 461 ILE cc_start: 0.8789 (mm) cc_final: 0.8571 (mm) REVERT: E 526 ASN cc_start: 0.9230 (m-40) cc_final: 0.8633 (p0) REVERT: E 623 ASP cc_start: 0.8142 (m-30) cc_final: 0.7129 (t0) REVERT: E 738 LEU cc_start: 0.9663 (mt) cc_final: 0.9211 (mp) REVERT: E 761 LEU cc_start: 0.8891 (mp) cc_final: 0.8527 (mp) REVERT: E 772 GLU cc_start: 0.9223 (mp0) cc_final: 0.8778 (mt-10) REVERT: F 51 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8497 (mmmt) REVERT: F 52 MET cc_start: 0.6929 (tpp) cc_final: 0.6458 (tpp) REVERT: F 133 THR cc_start: 0.9332 (m) cc_final: 0.9091 (p) REVERT: F 166 SER cc_start: 0.8272 (t) cc_final: 0.7999 (m) REVERT: F 308 TYR cc_start: 0.8575 (m-10) cc_final: 0.8035 (m-10) REVERT: F 343 MET cc_start: 0.8426 (mtp) cc_final: 0.8206 (mtt) REVERT: F 430 LEU cc_start: 0.8944 (tt) cc_final: 0.8521 (tp) REVERT: F 434 MET cc_start: 0.7516 (ptm) cc_final: 0.7246 (ptm) REVERT: F 436 SER cc_start: 0.8390 (p) cc_final: 0.8184 (p) REVERT: F 440 ASP cc_start: 0.8646 (m-30) cc_final: 0.8341 (m-30) REVERT: F 449 GLU cc_start: 0.7839 (mp0) cc_final: 0.7620 (mp0) REVERT: F 491 LEU cc_start: 0.9398 (mt) cc_final: 0.9023 (tp) REVERT: F 496 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7764 (mmm160) REVERT: F 540 LEU cc_start: 0.8544 (mt) cc_final: 0.8311 (tt) REVERT: F 590 MET cc_start: 0.6280 (ttt) cc_final: 0.5809 (ttt) REVERT: F 676 LYS cc_start: 0.8081 (pttt) cc_final: 0.7788 (tptt) REVERT: C 99 TYR cc_start: 0.6915 (m-80) cc_final: 0.5841 (m-80) REVERT: C 265 MET cc_start: 0.8957 (mmt) cc_final: 0.7856 (mmm) REVERT: C 343 MET cc_start: 0.8700 (mmm) cc_final: 0.8436 (tmm) REVERT: C 434 MET cc_start: 0.7730 (mmm) cc_final: 0.7363 (mmm) REVERT: C 461 ILE cc_start: 0.8734 (mm) cc_final: 0.8509 (mm) REVERT: C 468 LEU cc_start: 0.8760 (mp) cc_final: 0.8474 (mt) REVERT: C 506 LYS cc_start: 0.9281 (tptp) cc_final: 0.9077 (tptp) REVERT: C 526 ASN cc_start: 0.9273 (m-40) cc_final: 0.8088 (p0) REVERT: C 623 ASP cc_start: 0.8456 (m-30) cc_final: 0.7527 (t0) REVERT: C 772 GLU cc_start: 0.9293 (mp0) cc_final: 0.8875 (mt-10) REVERT: D 28 THR cc_start: 0.9221 (m) cc_final: 0.8940 (p) REVERT: D 166 SER cc_start: 0.8134 (t) cc_final: 0.7923 (m) REVERT: D 239 GLN cc_start: 0.8965 (mt0) cc_final: 0.8534 (pt0) REVERT: D 269 ILE cc_start: 0.8799 (mt) cc_final: 0.8505 (tp) REVERT: D 325 TYR cc_start: 0.9574 (t80) cc_final: 0.9140 (t80) REVERT: D 337 MET cc_start: 0.8580 (mmm) cc_final: 0.8186 (tmm) REVERT: D 430 LEU cc_start: 0.8982 (tt) cc_final: 0.8623 (tp) REVERT: D 436 SER cc_start: 0.8326 (p) cc_final: 0.8059 (p) REVERT: D 440 ASP cc_start: 0.8763 (m-30) cc_final: 0.8485 (m-30) REVERT: D 449 GLU cc_start: 0.7984 (mp0) cc_final: 0.7737 (mp0) REVERT: D 491 LEU cc_start: 0.9353 (mt) cc_final: 0.8949 (tp) REVERT: D 540 LEU cc_start: 0.8595 (mt) cc_final: 0.8243 (tt) REVERT: D 696 ASN cc_start: 0.9066 (m-40) cc_final: 0.8851 (p0) REVERT: D 775 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8778 (mt-10) REVERT: D 782 SER cc_start: 0.9307 (t) cc_final: 0.9082 (p) outliers start: 2 outliers final: 0 residues processed: 729 average time/residue: 0.2164 time to fit residues: 258.7872 Evaluate side-chains 410 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 4 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 chunk 271 optimal weight: 0.1980 chunk 219 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 118 optimal weight: 50.0000 chunk 110 optimal weight: 9.9990 chunk 363 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN B 287 HIS B 614 HIS E 625 ASN ** E 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 HIS F 614 HIS C 418 GLN ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 HIS D 287 HIS D 614 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.082540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.065035 restraints weight = 155741.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067158 restraints weight = 83010.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.068563 restraints weight = 51860.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069538 restraints weight = 36262.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070163 restraints weight = 27722.691| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35481 Z= 0.149 Angle : 0.720 10.755 48144 Z= 0.382 Chirality : 0.047 0.387 5616 Planarity : 0.004 0.063 5961 Dihedral : 4.928 25.136 4659 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.12 % 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: -1.62 (0.13), residues: 4257 helix: 0.06 (0.12), residues: 1911 sheet: -1.39 (0.22), residues: 585 loop : -2.23 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 550 TYR 0.032 0.002 TYR C 477 PHE 0.028 0.002 PHE C 156 TRP 0.029 0.002 TRP B 411 HIS 0.005 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00318 (35463) covalent geometry : angle 0.71955 (48108) SS BOND : bond 0.00430 ( 18) SS BOND : angle 1.34134 ( 36) hydrogen bonds : bond 0.05432 ( 1644) hydrogen bonds : angle 5.53615 ( 4401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 623 time to evaluate : 1.408 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: 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 35 MET cc_start: 0.9170 (mtp) cc_final: 0.8969 (mtp) REVERT: A 265 MET cc_start: 0.9065 (mmt) cc_final: 0.7851 (mmm) REVERT: A 343 MET cc_start: 0.8660 (mmm) cc_final: 0.8288 (mmm) REVERT: A 402 LEU cc_start: 0.9627 (tp) cc_final: 0.9326 (mt) REVERT: A 433 PHE cc_start: 0.8111 (p90) cc_final: 0.7839 (p90) REVERT: A 461 ILE cc_start: 0.8885 (mm) cc_final: 0.8681 (mm) REVERT: A 468 LEU cc_start: 0.8748 (mp) cc_final: 0.8472 (mt) REVERT: A 526 ASN cc_start: 0.9365 (m-40) cc_final: 0.8261 (p0) REVERT: A 623 ASP cc_start: 0.7945 (m-30) cc_final: 0.7178 (t0) REVERT: B 132 HIS cc_start: 0.9051 (m-70) cc_final: 0.8799 (m-70) REVERT: B 269 ILE cc_start: 0.9074 (mt) cc_final: 0.8811 (tp) REVERT: B 432 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8935 (mt) REVERT: B 473 GLU cc_start: 0.8297 (tt0) cc_final: 0.7975 (tt0) REVERT: B 519 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7850 (mm-30) REVERT: B 540 LEU cc_start: 0.8632 (mt) cc_final: 0.8300 (tt) REVERT: B 689 TYR cc_start: 0.7623 (m-80) cc_final: 0.7310 (m-10) REVERT: B 733 LEU cc_start: 0.8104 (tp) cc_final: 0.7778 (tp) REVERT: E 97 ILE cc_start: 0.7692 (mp) cc_final: 0.7384 (mp) REVERT: E 99 TYR cc_start: 0.6495 (m-80) cc_final: 0.5867 (m-80) REVERT: E 236 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8521 (mt-10) REVERT: E 261 TYR cc_start: 0.8341 (t80) cc_final: 0.8008 (t80) REVERT: E 265 MET cc_start: 0.9066 (mmt) cc_final: 0.7297 (mmm) REVERT: E 343 MET cc_start: 0.8696 (mmm) cc_final: 0.8182 (tmm) REVERT: E 433 PHE cc_start: 0.8208 (p90) cc_final: 0.7692 (p90) REVERT: E 434 MET cc_start: 0.7401 (mmm) cc_final: 0.7177 (mmm) REVERT: E 461 ILE cc_start: 0.8808 (mm) cc_final: 0.8592 (mm) REVERT: E 471 LEU cc_start: 0.9203 (tt) cc_final: 0.8985 (tt) REVERT: E 478 HIS cc_start: 0.7974 (m90) cc_final: 0.7771 (m90) REVERT: E 506 LYS cc_start: 0.9274 (tptp) cc_final: 0.9071 (tptp) REVERT: E 526 ASN cc_start: 0.9131 (m-40) cc_final: 0.8660 (p0) REVERT: E 623 ASP cc_start: 0.7837 (m-30) cc_final: 0.7308 (t0) REVERT: E 738 LEU cc_start: 0.9569 (mt) cc_final: 0.9262 (mp) REVERT: E 759 ILE cc_start: 0.8951 (mt) cc_final: 0.8725 (mm) REVERT: F 28 THR cc_start: 0.8706 (p) cc_final: 0.8483 (t) REVERT: F 51 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8544 (mmmt) REVERT: F 52 MET cc_start: 0.6893 (tpp) cc_final: 0.5720 (tpt) REVERT: F 133 THR cc_start: 0.9470 (m) cc_final: 0.9105 (m) REVERT: F 166 SER cc_start: 0.8278 (t) cc_final: 0.7938 (m) REVERT: F 308 TYR cc_start: 0.8592 (m-10) cc_final: 0.8029 (m-10) REVERT: F 430 LEU cc_start: 0.8873 (tt) cc_final: 0.8545 (tp) REVERT: F 434 MET cc_start: 0.7368 (ptm) cc_final: 0.6904 (ptm) REVERT: F 440 ASP cc_start: 0.8612 (m-30) cc_final: 0.8340 (m-30) REVERT: F 473 GLU cc_start: 0.8230 (tt0) cc_final: 0.8028 (tt0) REVERT: F 491 LEU cc_start: 0.9542 (mt) cc_final: 0.9130 (tp) REVERT: F 496 ARG cc_start: 0.8024 (mmt-90) cc_final: 0.7507 (mmp-170) REVERT: F 676 LYS cc_start: 0.8107 (pttt) cc_final: 0.7772 (tptt) REVERT: F 736 LEU cc_start: 0.9361 (tp) cc_final: 0.9119 (tp) REVERT: C 35 MET cc_start: 0.9297 (mtp) cc_final: 0.8824 (mtp) REVERT: C 52 MET cc_start: 0.8192 (mmm) cc_final: 0.7868 (tpt) REVERT: C 99 TYR cc_start: 0.6419 (m-80) cc_final: 0.5725 (m-80) REVERT: C 261 TYR cc_start: 0.8488 (t80) cc_final: 0.8153 (t80) REVERT: C 265 MET cc_start: 0.8990 (mmt) cc_final: 0.7334 (mmm) REVERT: C 343 MET cc_start: 0.8558 (mmm) cc_final: 0.8276 (tmm) REVERT: C 433 PHE cc_start: 0.8029 (p90) cc_final: 0.7649 (p90) REVERT: C 434 MET cc_start: 0.7695 (mmm) cc_final: 0.7300 (mmm) REVERT: C 461 ILE cc_start: 0.8761 (mm) cc_final: 0.8547 (mm) REVERT: C 471 LEU cc_start: 0.9224 (tp) cc_final: 0.8982 (tt) REVERT: C 493 GLU cc_start: 0.8926 (pt0) cc_final: 0.8623 (tm-30) REVERT: C 495 LEU cc_start: 0.8263 (mt) cc_final: 0.8006 (mt) REVERT: C 506 LYS cc_start: 0.9305 (tptp) cc_final: 0.9082 (mmtm) REVERT: C 518 LEU cc_start: 0.8291 (tp) cc_final: 0.8089 (tp) REVERT: C 526 ASN cc_start: 0.9206 (m-40) cc_final: 0.7991 (p0) REVERT: C 623 ASP cc_start: 0.8100 (m-30) cc_final: 0.7488 (t0) REVERT: C 651 ILE cc_start: 0.9454 (pt) cc_final: 0.9152 (tp) REVERT: C 710 LEU cc_start: 0.8793 (mt) cc_final: 0.8590 (mt) REVERT: C 738 LEU cc_start: 0.9623 (mp) cc_final: 0.9243 (mt) REVERT: D 28 THR cc_start: 0.9186 (m) cc_final: 0.8653 (t) REVERT: D 52 MET cc_start: 0.6908 (mmp) cc_final: 0.6366 (mmm) REVERT: D 166 SER cc_start: 0.8095 (t) cc_final: 0.7871 (m) REVERT: D 239 GLN cc_start: 0.8944 (mt0) cc_final: 0.8523 (pt0) REVERT: D 265 MET cc_start: 0.8495 (mmm) cc_final: 0.8243 (tpp) REVERT: D 325 TYR cc_start: 0.9534 (t80) cc_final: 0.9064 (t80) REVERT: D 337 MET cc_start: 0.8496 (mmm) cc_final: 0.8169 (tmm) REVERT: D 473 GLU cc_start: 0.8370 (tt0) cc_final: 0.7994 (tt0) REVERT: D 540 LEU cc_start: 0.8583 (mt) cc_final: 0.8354 (tt) REVERT: D 676 LYS cc_start: 0.8240 (pttt) cc_final: 0.7785 (tptp) REVERT: D 696 ASN cc_start: 0.9003 (m-40) cc_final: 0.8748 (p0) outliers start: 3 outliers final: 0 residues processed: 624 average time/residue: 0.2090 time to fit residues: 217.1872 Evaluate side-chains 401 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 371 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 425 optimal weight: 40.0000 chunk 304 optimal weight: 1.9990 chunk 141 optimal weight: 40.0000 chunk 367 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 200 optimal weight: 0.7980 chunk 378 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 625 ASN ** E 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS C 418 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN ** C 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064843 restraints weight = 157474.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066868 restraints weight = 84647.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068246 restraints weight = 53354.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069171 restraints weight = 37621.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.069790 restraints weight = 28880.490| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35481 Z= 0.138 Angle : 0.674 13.959 48144 Z= 0.356 Chirality : 0.046 0.407 5616 Planarity : 0.004 0.045 5961 Dihedral : 4.850 28.445 4659 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % 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: -1.65 (0.13), residues: 4257 helix: 0.09 (0.12), residues: 1902 sheet: -1.47 (0.21), residues: 591 loop : -2.27 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 550 TYR 0.033 0.002 TYR C 477 PHE 0.050 0.002 PHE D 250 TRP 0.028 0.002 TRP F 143 HIS 0.010 0.001 HIS E 499 Details of bonding type rmsd covalent geometry : bond 0.00295 (35463) covalent geometry : angle 0.67349 (48108) SS BOND : bond 0.00411 ( 18) SS BOND : angle 1.15285 ( 36) hydrogen bonds : bond 0.04884 ( 1644) hydrogen bonds : angle 5.27964 ( 4401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 583 time to evaluate : 1.562 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: 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: A 164 PHE cc_start: 0.8407 (t80) cc_final: 0.8099 (t80) REVERT: A 375 MET cc_start: 0.9154 (ptp) cc_final: 0.8937 (ptp) REVERT: A 380 ASP cc_start: 0.8421 (t0) cc_final: 0.7773 (m-30) REVERT: A 433 PHE cc_start: 0.7783 (p90) cc_final: 0.7544 (p90) REVERT: A 461 ILE cc_start: 0.8907 (mm) cc_final: 0.8676 (mm) REVERT: A 471 LEU cc_start: 0.9177 (tp) cc_final: 0.8955 (tp) REVERT: A 526 ASN cc_start: 0.9185 (m-40) cc_final: 0.8141 (p0) REVERT: A 623 ASP cc_start: 0.7862 (m-30) cc_final: 0.7113 (t0) REVERT: A 651 ILE cc_start: 0.9315 (pt) cc_final: 0.8970 (tp) REVERT: A 738 LEU cc_start: 0.9601 (mp) cc_final: 0.9163 (mp) REVERT: A 761 LEU cc_start: 0.8848 (mp) cc_final: 0.8561 (mp) REVERT: B 35 MET cc_start: 0.9192 (mtp) cc_final: 0.8925 (mtm) REVERT: B 52 MET cc_start: 0.6262 (tpt) cc_final: 0.5016 (tpt) REVERT: B 133 THR cc_start: 0.9414 (m) cc_final: 0.8955 (m) REVERT: B 308 TYR cc_start: 0.8789 (m-80) cc_final: 0.8331 (m-80) REVERT: B 436 SER cc_start: 0.8594 (p) cc_final: 0.8378 (p) REVERT: B 491 LEU cc_start: 0.9443 (mt) cc_final: 0.8931 (tp) REVERT: B 540 LEU cc_start: 0.8664 (mt) cc_final: 0.8333 (tt) REVERT: B 573 SER cc_start: 0.7389 (t) cc_final: 0.6818 (p) REVERT: B 689 TYR cc_start: 0.7475 (m-80) cc_final: 0.7212 (m-10) REVERT: B 733 LEU cc_start: 0.8207 (tp) cc_final: 0.7884 (tp) REVERT: E 35 MET cc_start: 0.9317 (mtp) cc_final: 0.9009 (mtp) REVERT: E 52 MET cc_start: 0.8067 (mmm) cc_final: 0.7821 (tpt) REVERT: E 236 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8502 (mt-10) REVERT: E 325 TYR cc_start: 0.9232 (t80) cc_final: 0.8698 (t80) REVERT: E 375 MET cc_start: 0.9237 (ptp) cc_final: 0.8872 (ptp) REVERT: E 434 MET cc_start: 0.7370 (mmm) cc_final: 0.7132 (mmm) REVERT: E 461 ILE cc_start: 0.8876 (mm) cc_final: 0.8661 (mm) REVERT: E 471 LEU cc_start: 0.9244 (tt) cc_final: 0.9015 (tt) REVERT: E 506 LYS cc_start: 0.9279 (tptp) cc_final: 0.8992 (tptp) REVERT: E 526 ASN cc_start: 0.9111 (m-40) cc_final: 0.8640 (p0) REVERT: E 623 ASP cc_start: 0.7954 (m-30) cc_final: 0.7450 (t0) REVERT: E 710 LEU cc_start: 0.8700 (mt) cc_final: 0.8403 (mt) REVERT: F 35 MET cc_start: 0.9234 (ttp) cc_final: 0.8858 (ttt) REVERT: F 51 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8557 (mmmt) REVERT: F 52 MET cc_start: 0.7041 (tpp) cc_final: 0.6589 (tpp) REVERT: F 166 SER cc_start: 0.8059 (t) cc_final: 0.7645 (m) REVERT: F 291 PHE cc_start: 0.7341 (t80) cc_final: 0.7053 (t80) REVERT: F 308 TYR cc_start: 0.8691 (m-10) cc_final: 0.7902 (m-10) REVERT: F 434 MET cc_start: 0.7495 (ptm) cc_final: 0.7272 (ptm) REVERT: F 491 LEU cc_start: 0.9509 (mt) cc_final: 0.9099 (tp) REVERT: F 496 ARG cc_start: 0.8020 (mmt-90) cc_final: 0.7438 (mmm160) REVERT: F 676 LYS cc_start: 0.8006 (pttt) cc_final: 0.7753 (tptt) REVERT: F 733 LEU cc_start: 0.8063 (tp) cc_final: 0.7846 (tp) REVERT: F 736 LEU cc_start: 0.9240 (tp) cc_final: 0.8929 (tt) REVERT: C 35 MET cc_start: 0.9329 (mtp) cc_final: 0.8879 (mtp) REVERT: C 52 MET cc_start: 0.7952 (mmm) cc_final: 0.7655 (tpt) REVERT: C 97 ILE cc_start: 0.7795 (mm) cc_final: 0.7415 (mp) REVERT: C 99 TYR cc_start: 0.6962 (m-80) cc_final: 0.6202 (m-80) REVERT: C 261 TYR cc_start: 0.8462 (t80) cc_final: 0.8155 (t80) REVERT: C 265 MET cc_start: 0.8955 (mmm) cc_final: 0.7865 (mmm) REVERT: C 328 LEU cc_start: 0.9669 (mm) cc_final: 0.9462 (mm) REVERT: C 434 MET cc_start: 0.7576 (mmm) cc_final: 0.7212 (mmt) REVERT: C 461 ILE cc_start: 0.8787 (mm) cc_final: 0.8580 (mm) REVERT: C 468 LEU cc_start: 0.8599 (mt) cc_final: 0.7954 (tp) REVERT: C 471 LEU cc_start: 0.9207 (tp) cc_final: 0.8794 (tt) REVERT: C 493 GLU cc_start: 0.8915 (pt0) cc_final: 0.8590 (tm-30) REVERT: C 495 LEU cc_start: 0.8278 (mt) cc_final: 0.8010 (mt) REVERT: C 506 LYS cc_start: 0.9327 (tptp) cc_final: 0.9033 (mmtm) REVERT: C 623 ASP cc_start: 0.8122 (m-30) cc_final: 0.7541 (t0) REVERT: C 651 ILE cc_start: 0.9433 (pt) cc_final: 0.9196 (tp) REVERT: C 710 LEU cc_start: 0.8911 (mt) cc_final: 0.8663 (mt) REVERT: C 738 LEU cc_start: 0.9501 (mp) cc_final: 0.9252 (mp) REVERT: D 28 THR cc_start: 0.9145 (m) cc_final: 0.8638 (t) REVERT: D 239 GLN cc_start: 0.8875 (mt0) cc_final: 0.8488 (pt0) REVERT: D 308 TYR cc_start: 0.8654 (m-80) cc_final: 0.8035 (m-80) REVERT: D 337 MET cc_start: 0.8540 (mmm) cc_final: 0.8106 (tmm) REVERT: D 434 MET cc_start: 0.7768 (ptm) cc_final: 0.7483 (ptm) REVERT: D 473 GLU cc_start: 0.8369 (tt0) cc_final: 0.7988 (tt0) REVERT: D 491 LEU cc_start: 0.9428 (tp) cc_final: 0.9218 (tp) REVERT: D 540 LEU cc_start: 0.8625 (mt) cc_final: 0.8402 (tt) REVERT: D 676 LYS cc_start: 0.8199 (pttt) cc_final: 0.7877 (tppt) REVERT: D 696 ASN cc_start: 0.8945 (m-40) cc_final: 0.8736 (p0) outliers start: 1 outliers final: 0 residues processed: 584 average time/residue: 0.1984 time to fit residues: 194.3746 Evaluate side-chains 400 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 119 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 26 optimal weight: 0.0020 chunk 352 optimal weight: 20.0000 chunk 99 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 371 optimal weight: 4.9990 chunk 420 optimal weight: 3.9990 chunk 113 optimal weight: 0.0980 chunk 14 optimal weight: 9.9990 chunk 319 optimal weight: 8.9990 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.080693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063266 restraints weight = 162060.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065263 restraints weight = 87685.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066621 restraints weight = 55539.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067517 restraints weight = 39257.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068147 restraints weight = 30340.774| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35481 Z= 0.136 Angle : 0.657 13.403 48144 Z= 0.346 Chirality : 0.045 0.329 5616 Planarity : 0.004 0.046 5961 Dihedral : 4.751 25.881 4659 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -1.62 (0.13), residues: 4257 helix: 0.15 (0.12), residues: 1887 sheet: -1.47 (0.21), residues: 591 loop : -2.27 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 600 TYR 0.028 0.002 TYR E 477 PHE 0.036 0.002 PHE B 250 TRP 0.036 0.002 TRP F 143 HIS 0.012 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00293 (35463) covalent geometry : angle 0.65685 (48108) SS BOND : bond 0.00552 ( 18) SS BOND : angle 1.10860 ( 36) hydrogen bonds : bond 0.04535 ( 1644) hydrogen bonds : angle 5.16368 ( 4401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 1.391 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9097 (mtp) cc_final: 0.8625 (mtm) REVERT: A 164 PHE cc_start: 0.8442 (t80) cc_final: 0.8164 (t80) REVERT: A 265 MET cc_start: 0.9083 (tpp) cc_final: 0.8879 (mmp) REVERT: A 380 ASP cc_start: 0.8409 (t0) cc_final: 0.7761 (m-30) REVERT: A 433 PHE cc_start: 0.8130 (p90) cc_final: 0.7614 (p90) REVERT: A 434 MET cc_start: 0.6918 (mmp) cc_final: 0.6615 (mmp) REVERT: A 461 ILE cc_start: 0.8923 (mm) cc_final: 0.8714 (mm) REVERT: A 468 LEU cc_start: 0.8717 (mt) cc_final: 0.7941 (tt) REVERT: A 471 LEU cc_start: 0.9180 (tp) cc_final: 0.8690 (tt) REVERT: A 526 ASN cc_start: 0.9164 (m-40) cc_final: 0.8132 (p0) REVERT: A 623 ASP cc_start: 0.8078 (m-30) cc_final: 0.7303 (t0) REVERT: A 738 LEU cc_start: 0.9520 (mp) cc_final: 0.9287 (mp) REVERT: B 35 MET cc_start: 0.9159 (mtp) cc_final: 0.8937 (mtm) REVERT: B 52 MET cc_start: 0.6895 (tpt) cc_final: 0.5670 (tpt) REVERT: B 133 THR cc_start: 0.9440 (m) cc_final: 0.9069 (m) REVERT: B 239 GLN cc_start: 0.8689 (mt0) cc_final: 0.8371 (tt0) REVERT: B 308 TYR cc_start: 0.8890 (m-80) cc_final: 0.8385 (m-80) REVERT: B 491 LEU cc_start: 0.9463 (mt) cc_final: 0.8950 (tp) REVERT: B 520 GLU cc_start: 0.8818 (tt0) cc_final: 0.8482 (tt0) REVERT: B 540 LEU cc_start: 0.8689 (mt) cc_final: 0.8415 (tt) REVERT: B 689 TYR cc_start: 0.7692 (m-80) cc_final: 0.7424 (m-10) REVERT: B 733 LEU cc_start: 0.8254 (tp) cc_final: 0.7653 (tp) REVERT: E 36 LEU cc_start: 0.9543 (tt) cc_final: 0.9212 (tp) REVERT: E 52 MET cc_start: 0.8032 (mmm) cc_final: 0.7828 (tpt) REVERT: E 236 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8404 (mt-10) REVERT: E 375 MET cc_start: 0.9203 (ptp) cc_final: 0.8979 (ptp) REVERT: E 433 PHE cc_start: 0.8310 (p90) cc_final: 0.7701 (p90) REVERT: E 434 MET cc_start: 0.7733 (mmm) cc_final: 0.7509 (mmm) REVERT: E 468 LEU cc_start: 0.8578 (mt) cc_final: 0.7700 (tt) REVERT: E 471 LEU cc_start: 0.9205 (tt) cc_final: 0.8708 (tt) REVERT: E 526 ASN cc_start: 0.9165 (m-40) cc_final: 0.8653 (p0) REVERT: E 623 ASP cc_start: 0.8062 (m-30) cc_final: 0.7467 (t0) REVERT: F 52 MET cc_start: 0.6988 (tpp) cc_final: 0.6468 (tpp) REVERT: F 133 THR cc_start: 0.9212 (m) cc_final: 0.8881 (m) REVERT: F 166 SER cc_start: 0.8194 (t) cc_final: 0.7828 (m) REVERT: F 291 PHE cc_start: 0.7417 (t80) cc_final: 0.7118 (t80) REVERT: F 308 TYR cc_start: 0.8751 (m-10) cc_final: 0.7695 (m-10) REVERT: F 496 ARG cc_start: 0.8071 (mmt-90) cc_final: 0.7569 (mmm160) REVERT: F 676 LYS cc_start: 0.8118 (pttt) cc_final: 0.7820 (tptt) REVERT: F 733 LEU cc_start: 0.7806 (tp) cc_final: 0.7538 (tp) REVERT: C 35 MET cc_start: 0.9350 (mtp) cc_final: 0.8995 (mtp) REVERT: C 52 MET cc_start: 0.7908 (mmm) cc_final: 0.7583 (tpt) REVERT: C 265 MET cc_start: 0.9150 (mmm) cc_final: 0.8819 (mmm) REVERT: C 434 MET cc_start: 0.7734 (mmm) cc_final: 0.7452 (mmp) REVERT: C 461 ILE cc_start: 0.8859 (mm) cc_final: 0.8642 (mm) REVERT: C 468 LEU cc_start: 0.8595 (mt) cc_final: 0.7859 (tt) REVERT: C 471 LEU cc_start: 0.9268 (tp) cc_final: 0.8803 (tt) REVERT: C 493 GLU cc_start: 0.8934 (pt0) cc_final: 0.8602 (tm-30) REVERT: C 506 LYS cc_start: 0.9365 (tptp) cc_final: 0.9056 (mmtm) REVERT: C 623 ASP cc_start: 0.8204 (m-30) cc_final: 0.7692 (t0) REVERT: C 651 ILE cc_start: 0.9453 (pt) cc_final: 0.9206 (tp) REVERT: C 710 LEU cc_start: 0.8969 (mt) cc_final: 0.8680 (mt) REVERT: D 28 THR cc_start: 0.9028 (m) cc_final: 0.8552 (t) REVERT: D 239 GLN cc_start: 0.8878 (mt0) cc_final: 0.8341 (pt0) REVERT: D 308 TYR cc_start: 0.8730 (m-80) cc_final: 0.8112 (m-80) REVERT: D 337 MET cc_start: 0.8591 (mmm) cc_final: 0.8121 (tmm) REVERT: D 434 MET cc_start: 0.7731 (ptm) cc_final: 0.7467 (ptm) REVERT: D 473 GLU cc_start: 0.8548 (tt0) cc_final: 0.8180 (tt0) REVERT: D 491 LEU cc_start: 0.9471 (tp) cc_final: 0.9143 (tp) REVERT: D 546 LEU cc_start: 0.9509 (tp) cc_final: 0.9035 (pp) REVERT: D 593 LEU cc_start: 0.8442 (mt) cc_final: 0.8149 (mp) REVERT: D 676 LYS cc_start: 0.8188 (pttt) cc_final: 0.7879 (tppt) REVERT: D 733 LEU cc_start: 0.8076 (tp) cc_final: 0.7768 (tp) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.2055 time to fit residues: 185.5336 Evaluate side-chains 370 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 318 optimal weight: 3.9990 chunk 395 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 294 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 369 optimal weight: 20.0000 chunk 217 optimal weight: 0.0870 chunk 365 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN F 141 ASN C 418 GLN C 499 HIS C 522 HIS C 663 ASN D 105 GLN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.081744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.064419 restraints weight = 159116.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066477 restraints weight = 85651.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067853 restraints weight = 53945.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.068750 restraints weight = 38011.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.069406 restraints weight = 29392.167| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35481 Z= 0.119 Angle : 0.652 14.607 48144 Z= 0.335 Chirality : 0.045 0.347 5616 Planarity : 0.004 0.044 5961 Dihedral : 4.645 26.898 4659 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.08 % Allowed : 1.85 % Favored : 98.07 % 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: -1.58 (0.13), residues: 4257 helix: 0.20 (0.12), residues: 1887 sheet: -1.40 (0.22), residues: 588 loop : -2.30 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 550 TYR 0.037 0.002 TYR C 477 PHE 0.033 0.002 PHE B 250 TRP 0.036 0.002 TRP C 647 HIS 0.005 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00245 (35463) covalent geometry : angle 0.65135 (48108) SS BOND : bond 0.00402 ( 18) SS BOND : angle 1.19730 ( 36) hydrogen bonds : bond 0.04240 ( 1644) hydrogen bonds : angle 4.97217 ( 4401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 523 time to evaluate : 1.247 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: 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: A 164 PHE cc_start: 0.8444 (t80) cc_final: 0.8156 (t80) REVERT: A 325 TYR cc_start: 0.9379 (t80) cc_final: 0.9176 (t80) REVERT: A 337 MET cc_start: 0.8971 (mmp) cc_final: 0.7591 (tmm) REVERT: A 468 LEU cc_start: 0.8701 (mt) cc_final: 0.7910 (tt) REVERT: A 471 LEU cc_start: 0.9193 (tp) cc_final: 0.8713 (tt) REVERT: A 526 ASN cc_start: 0.9145 (m-40) cc_final: 0.8105 (p0) REVERT: A 623 ASP cc_start: 0.8015 (m-30) cc_final: 0.7278 (t0) REVERT: A 651 ILE cc_start: 0.9321 (pt) cc_final: 0.9062 (tp) REVERT: B 35 MET cc_start: 0.9171 (mtp) cc_final: 0.8920 (mtm) REVERT: B 52 MET cc_start: 0.6957 (tpt) cc_final: 0.5556 (tpt) REVERT: B 133 THR cc_start: 0.9461 (m) cc_final: 0.9209 (m) REVERT: B 239 GLN cc_start: 0.8752 (mt0) cc_final: 0.8294 (tt0) REVERT: B 308 TYR cc_start: 0.8851 (m-80) cc_final: 0.8299 (m-80) REVERT: B 491 LEU cc_start: 0.9434 (mt) cc_final: 0.9087 (tp) REVERT: B 520 GLU cc_start: 0.8801 (tt0) cc_final: 0.8433 (tt0) REVERT: B 733 LEU cc_start: 0.8230 (tp) cc_final: 0.7602 (tp) REVERT: E 36 LEU cc_start: 0.9544 (tt) cc_final: 0.9281 (tp) REVERT: E 164 PHE cc_start: 0.8496 (t80) cc_final: 0.8162 (t80) REVERT: E 236 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8404 (mt-10) REVERT: E 375 MET cc_start: 0.9250 (ptp) cc_final: 0.9016 (ptp) REVERT: E 433 PHE cc_start: 0.8263 (p90) cc_final: 0.7722 (p90) REVERT: E 434 MET cc_start: 0.7695 (mmm) cc_final: 0.7405 (mmm) REVERT: E 526 ASN cc_start: 0.9106 (m-40) cc_final: 0.8597 (p0) REVERT: E 623 ASP cc_start: 0.7986 (m-30) cc_final: 0.7366 (t0) REVERT: E 691 ASP cc_start: 0.8296 (t0) cc_final: 0.8070 (t0) REVERT: F 52 MET cc_start: 0.6923 (tpp) cc_final: 0.6621 (tpp) REVERT: F 166 SER cc_start: 0.8184 (t) cc_final: 0.7839 (m) REVERT: F 291 PHE cc_start: 0.7100 (t80) cc_final: 0.6769 (t80) REVERT: F 308 TYR cc_start: 0.8728 (m-10) cc_final: 0.7531 (m-10) REVERT: F 473 GLU cc_start: 0.8399 (tt0) cc_final: 0.8169 (tt0) REVERT: F 495 LEU cc_start: 0.9286 (mt) cc_final: 0.9042 (mt) REVERT: F 496 ARG cc_start: 0.8038 (mmt-90) cc_final: 0.7513 (mmm160) REVERT: F 733 LEU cc_start: 0.7994 (tp) cc_final: 0.7773 (tp) REVERT: C 35 MET cc_start: 0.9334 (mtp) cc_final: 0.8904 (mtp) REVERT: C 52 MET cc_start: 0.7897 (mmm) cc_final: 0.7554 (tpt) REVERT: C 265 MET cc_start: 0.9016 (mmm) cc_final: 0.8660 (mmm) REVERT: C 433 PHE cc_start: 0.8227 (p90) cc_final: 0.7598 (p90) REVERT: C 471 LEU cc_start: 0.9271 (tp) cc_final: 0.9001 (tt) REVERT: C 506 LYS cc_start: 0.9349 (tptp) cc_final: 0.9061 (mmtm) REVERT: C 526 ASN cc_start: 0.8919 (m-40) cc_final: 0.7960 (p0) REVERT: C 623 ASP cc_start: 0.8117 (m-30) cc_final: 0.7564 (t0) REVERT: C 651 ILE cc_start: 0.9427 (pt) cc_final: 0.9168 (tp) REVERT: D 28 THR cc_start: 0.9147 (m) cc_final: 0.8651 (t) REVERT: D 52 MET cc_start: 0.6974 (tpp) cc_final: 0.5652 (tpt) REVERT: D 53 ILE cc_start: 0.9331 (mm) cc_final: 0.9045 (mm) REVERT: D 239 GLN cc_start: 0.8894 (mt0) cc_final: 0.8467 (pt0) REVERT: D 308 TYR cc_start: 0.8645 (m-80) cc_final: 0.7971 (m-80) REVERT: D 337 MET cc_start: 0.8598 (mmm) cc_final: 0.8096 (tmm) REVERT: D 434 MET cc_start: 0.7793 (ptm) cc_final: 0.7564 (ptm) REVERT: D 473 GLU cc_start: 0.8458 (tt0) cc_final: 0.8107 (tt0) REVERT: D 491 LEU cc_start: 0.9410 (tp) cc_final: 0.9177 (tp) REVERT: D 546 LEU cc_start: 0.9590 (tp) cc_final: 0.9021 (pp) REVERT: D 676 LYS cc_start: 0.8197 (pttt) cc_final: 0.7882 (tppt) REVERT: D 733 LEU cc_start: 0.8104 (tp) cc_final: 0.7844 (tp) outliers start: 3 outliers final: 0 residues processed: 525 average time/residue: 0.2015 time to fit residues: 178.2357 Evaluate side-chains 377 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 326 optimal weight: 7.9990 chunk 407 optimal weight: 6.9990 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 265 optimal weight: 5.9990 chunk 348 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 269 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN F 49 GLN C 104 HIS C 418 GLN C 568 HIS D 49 GLN D 105 GLN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.080096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062701 restraints weight = 161725.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.064670 restraints weight = 87624.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065998 restraints weight = 55717.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066891 restraints weight = 39606.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067511 restraints weight = 30607.644| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 35481 Z= 0.146 Angle : 0.654 13.213 48144 Z= 0.343 Chirality : 0.045 0.308 5616 Planarity : 0.004 0.045 5961 Dihedral : 4.639 26.117 4659 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 4257 helix: 0.16 (0.12), residues: 1887 sheet: -1.37 (0.21), residues: 588 loop : -2.34 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 605 TYR 0.041 0.002 TYR C 477 PHE 0.037 0.002 PHE D 244 TRP 0.027 0.002 TRP F 511 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00317 (35463) covalent geometry : angle 0.65346 (48108) SS BOND : bond 0.00559 ( 18) SS BOND : angle 1.33513 ( 36) hydrogen bonds : bond 0.04238 ( 1644) hydrogen bonds : angle 4.99993 ( 4401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 470 time to evaluate : 1.448 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: 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: A 164 PHE cc_start: 0.8588 (t80) cc_final: 0.8315 (t80) REVERT: A 265 MET cc_start: 0.9003 (tpp) cc_final: 0.8740 (mmp) REVERT: A 433 PHE cc_start: 0.8116 (p90) cc_final: 0.7556 (p90) REVERT: A 448 LEU cc_start: 0.8747 (tp) cc_final: 0.8507 (tt) REVERT: A 506 LYS cc_start: 0.9368 (tppt) cc_final: 0.9141 (mmtm) REVERT: A 526 ASN cc_start: 0.9208 (m-40) cc_final: 0.8198 (p0) REVERT: A 623 ASP cc_start: 0.8026 (m-30) cc_final: 0.7286 (t0) REVERT: B 52 MET cc_start: 0.6941 (tpt) cc_final: 0.5574 (tpt) REVERT: B 133 THR cc_start: 0.9486 (m) cc_final: 0.9284 (m) REVERT: B 239 GLN cc_start: 0.8832 (mt0) cc_final: 0.8439 (pt0) REVERT: B 308 TYR cc_start: 0.8970 (m-80) cc_final: 0.8469 (m-80) REVERT: B 491 LEU cc_start: 0.9454 (mt) cc_final: 0.9088 (tp) REVERT: B 501 LYS cc_start: 0.8804 (tptp) cc_final: 0.8580 (mmmt) REVERT: B 520 GLU cc_start: 0.8806 (tt0) cc_final: 0.8458 (tt0) REVERT: B 733 LEU cc_start: 0.8260 (tp) cc_final: 0.7573 (tp) REVERT: E 35 MET cc_start: 0.9246 (mtp) cc_final: 0.9029 (mtm) REVERT: E 36 LEU cc_start: 0.9537 (tt) cc_final: 0.9294 (tp) REVERT: E 52 MET cc_start: 0.7859 (tpt) cc_final: 0.7652 (tpt) REVERT: E 164 PHE cc_start: 0.8543 (t80) cc_final: 0.8229 (t80) REVERT: E 236 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8400 (mt-10) REVERT: E 325 TYR cc_start: 0.9277 (t80) cc_final: 0.8995 (t80) REVERT: E 433 PHE cc_start: 0.8046 (p90) cc_final: 0.7833 (p90) REVERT: E 468 LEU cc_start: 0.8534 (mt) cc_final: 0.7712 (tp) REVERT: E 471 LEU cc_start: 0.9249 (tt) cc_final: 0.8802 (tt) REVERT: E 526 ASN cc_start: 0.9101 (m-40) cc_final: 0.8596 (p0) REVERT: E 623 ASP cc_start: 0.7988 (m-30) cc_final: 0.7395 (t0) REVERT: E 635 PHE cc_start: 0.7475 (t80) cc_final: 0.7267 (t80) REVERT: E 691 ASP cc_start: 0.8247 (t0) cc_final: 0.8002 (t0) REVERT: F 52 MET cc_start: 0.6939 (tpp) cc_final: 0.6521 (tpp) REVERT: F 166 SER cc_start: 0.8206 (t) cc_final: 0.7818 (m) REVERT: F 324 PHE cc_start: 0.9233 (t80) cc_final: 0.8967 (t80) REVERT: F 473 GLU cc_start: 0.8351 (tt0) cc_final: 0.8121 (tt0) REVERT: F 496 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7481 (mmm160) REVERT: F 676 LYS cc_start: 0.8138 (pttt) cc_final: 0.7830 (tptt) REVERT: F 733 LEU cc_start: 0.8091 (tp) cc_final: 0.7671 (tp) REVERT: C 35 MET cc_start: 0.9310 (mtp) cc_final: 0.8932 (mtp) REVERT: C 52 MET cc_start: 0.8012 (mmm) cc_final: 0.7634 (tpt) REVERT: C 99 TYR cc_start: 0.6836 (m-80) cc_final: 0.6509 (m-80) REVERT: C 265 MET cc_start: 0.9033 (mmm) cc_final: 0.8645 (mmm) REVERT: C 308 TYR cc_start: 0.8881 (m-10) cc_final: 0.8578 (m-10) REVERT: C 433 PHE cc_start: 0.8537 (p90) cc_final: 0.7733 (p90) REVERT: C 434 MET cc_start: 0.7408 (mmp) cc_final: 0.6926 (mmp) REVERT: C 471 LEU cc_start: 0.9316 (tp) cc_final: 0.9013 (tt) REVERT: C 506 LYS cc_start: 0.9379 (tptp) cc_final: 0.9099 (mmtm) REVERT: C 526 ASN cc_start: 0.9023 (m-40) cc_final: 0.8004 (p0) REVERT: C 623 ASP cc_start: 0.8161 (m-30) cc_final: 0.7603 (t0) REVERT: C 651 ILE cc_start: 0.9432 (pt) cc_final: 0.9206 (tp) REVERT: C 710 LEU cc_start: 0.8720 (mt) cc_final: 0.8447 (mt) REVERT: D 28 THR cc_start: 0.9104 (m) cc_final: 0.8583 (t) REVERT: D 239 GLN cc_start: 0.8995 (mt0) cc_final: 0.8487 (pt0) REVERT: D 308 TYR cc_start: 0.8743 (m-80) cc_final: 0.8273 (m-80) REVERT: D 337 MET cc_start: 0.8618 (mmm) cc_final: 0.8107 (tmm) REVERT: D 434 MET cc_start: 0.7797 (ptm) cc_final: 0.7563 (ptm) REVERT: D 473 GLU cc_start: 0.8423 (tt0) cc_final: 0.8086 (tt0) REVERT: D 491 LEU cc_start: 0.9418 (tp) cc_final: 0.9133 (tp) REVERT: D 546 LEU cc_start: 0.9595 (tp) cc_final: 0.9327 (tp) REVERT: D 676 LYS cc_start: 0.8180 (pttt) cc_final: 0.7906 (tppt) outliers start: 1 outliers final: 0 residues processed: 471 average time/residue: 0.2061 time to fit residues: 162.0808 Evaluate side-chains 353 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 191 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 392 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 101 optimal weight: 0.0970 chunk 207 optimal weight: 5.9990 chunk 309 optimal weight: 8.9990 chunk 262 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 166 optimal weight: 0.0870 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 568 HIS ** C 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.081006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.063669 restraints weight = 161327.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065681 restraints weight = 87328.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.067009 restraints weight = 55250.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067925 restraints weight = 39159.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.068502 restraints weight = 30353.425| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 35481 Z= 0.119 Angle : 0.652 15.377 48144 Z= 0.335 Chirality : 0.045 0.297 5616 Planarity : 0.004 0.062 5961 Dihedral : 4.574 26.292 4659 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.03 % Allowed : 0.95 % Favored : 99.02 % 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: -1.54 (0.13), residues: 4257 helix: 0.27 (0.12), residues: 1872 sheet: -1.37 (0.21), residues: 588 loop : -2.30 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 550 TYR 0.036 0.001 TYR C 477 PHE 0.036 0.002 PHE B 250 TRP 0.026 0.002 TRP F 511 HIS 0.008 0.001 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00249 (35463) covalent geometry : angle 0.65123 (48108) SS BOND : bond 0.00706 ( 18) SS BOND : angle 1.31368 ( 36) hydrogen bonds : bond 0.04036 ( 1644) hydrogen bonds : angle 4.88771 ( 4401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 490 time to evaluate : 1.672 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: 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 36 LEU cc_start: 0.9546 (tt) cc_final: 0.9195 (tp) REVERT: A 164 PHE cc_start: 0.8598 (t80) cc_final: 0.8301 (t80) REVERT: A 337 MET cc_start: 0.8790 (mmp) cc_final: 0.7553 (tmm) REVERT: A 433 PHE cc_start: 0.8110 (p90) cc_final: 0.7629 (p90) REVERT: A 455 LEU cc_start: 0.8978 (mm) cc_final: 0.8579 (mm) REVERT: A 468 LEU cc_start: 0.8617 (mt) cc_final: 0.7692 (tt) REVERT: A 526 ASN cc_start: 0.9212 (m-40) cc_final: 0.8234 (p0) REVERT: A 623 ASP cc_start: 0.8012 (m-30) cc_final: 0.7251 (t0) REVERT: A 635 PHE cc_start: 0.7570 (t80) cc_final: 0.7333 (t80) REVERT: B 52 MET cc_start: 0.6825 (tpt) cc_final: 0.6228 (tpt) REVERT: B 308 TYR cc_start: 0.8951 (m-80) cc_final: 0.8252 (m-80) REVERT: B 491 LEU cc_start: 0.9443 (mt) cc_final: 0.8864 (tp) REVERT: B 495 LEU cc_start: 0.9283 (mp) cc_final: 0.8913 (mp) REVERT: B 520 GLU cc_start: 0.8743 (tt0) cc_final: 0.8414 (tt0) REVERT: B 573 SER cc_start: 0.7372 (t) cc_final: 0.6608 (t) REVERT: B 733 LEU cc_start: 0.8195 (tp) cc_final: 0.7548 (tp) REVERT: E 36 LEU cc_start: 0.9535 (tt) cc_final: 0.9264 (tp) REVERT: E 52 MET cc_start: 0.7923 (tpt) cc_final: 0.7643 (tpt) REVERT: E 236 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8379 (mt-10) REVERT: E 375 MET cc_start: 0.9401 (ptp) cc_final: 0.9106 (ptp) REVERT: E 433 PHE cc_start: 0.8266 (p90) cc_final: 0.7539 (p90) REVERT: E 526 ASN cc_start: 0.9100 (m-40) cc_final: 0.8622 (p0) REVERT: E 623 ASP cc_start: 0.7950 (m-30) cc_final: 0.7376 (t0) REVERT: E 635 PHE cc_start: 0.7502 (t80) cc_final: 0.7286 (t80) REVERT: E 691 ASP cc_start: 0.8317 (t0) cc_final: 0.8063 (t0) REVERT: F 52 MET cc_start: 0.6729 (tpp) cc_final: 0.6367 (tpp) REVERT: F 166 SER cc_start: 0.8097 (t) cc_final: 0.7760 (m) REVERT: F 308 TYR cc_start: 0.9000 (m-10) cc_final: 0.8416 (m-80) REVERT: F 324 PHE cc_start: 0.9227 (t80) cc_final: 0.8989 (t80) REVERT: F 473 GLU cc_start: 0.8343 (tt0) cc_final: 0.8118 (tt0) REVERT: F 496 ARG cc_start: 0.7896 (mmt-90) cc_final: 0.7416 (mmm160) REVERT: F 676 LYS cc_start: 0.8122 (pttt) cc_final: 0.7846 (tptt) REVERT: F 733 LEU cc_start: 0.8108 (tp) cc_final: 0.7690 (tp) REVERT: C 35 MET cc_start: 0.9285 (mtp) cc_final: 0.9075 (mtp) REVERT: C 36 LEU cc_start: 0.9492 (tt) cc_final: 0.9121 (tp) REVERT: C 52 MET cc_start: 0.7924 (mmm) cc_final: 0.7644 (tpt) REVERT: C 265 MET cc_start: 0.9032 (mmm) cc_final: 0.8279 (mmm) REVERT: C 337 MET cc_start: 0.8888 (mmp) cc_final: 0.7729 (tmm) REVERT: C 433 PHE cc_start: 0.8519 (p90) cc_final: 0.7786 (p90) REVERT: C 434 MET cc_start: 0.7695 (mmp) cc_final: 0.7003 (mmp) REVERT: C 471 LEU cc_start: 0.9286 (tp) cc_final: 0.8968 (tt) REVERT: C 526 ASN cc_start: 0.9028 (m-40) cc_final: 0.8002 (p0) REVERT: C 623 ASP cc_start: 0.8153 (m-30) cc_final: 0.7545 (t0) REVERT: C 651 ILE cc_start: 0.9400 (pt) cc_final: 0.9150 (tp) REVERT: C 710 LEU cc_start: 0.8703 (mt) cc_final: 0.8435 (mt) REVERT: D 28 THR cc_start: 0.9076 (m) cc_final: 0.8566 (t) REVERT: D 52 MET cc_start: 0.6936 (tpp) cc_final: 0.5878 (tpt) REVERT: D 239 GLN cc_start: 0.8912 (mt0) cc_final: 0.8466 (pt0) REVERT: D 308 TYR cc_start: 0.8649 (m-80) cc_final: 0.8123 (m-80) REVERT: D 337 MET cc_start: 0.8630 (mmm) cc_final: 0.8118 (tmm) REVERT: D 375 MET cc_start: 0.7913 (ptp) cc_final: 0.7320 (ptp) REVERT: D 445 LEU cc_start: 0.8886 (mm) cc_final: 0.8646 (mm) REVERT: D 473 GLU cc_start: 0.8379 (tt0) cc_final: 0.8051 (tt0) REVERT: D 491 LEU cc_start: 0.9366 (tp) cc_final: 0.9045 (tp) REVERT: D 546 LEU cc_start: 0.9581 (tp) cc_final: 0.9326 (tp) REVERT: D 676 LYS cc_start: 0.8175 (pttt) cc_final: 0.7892 (tppt) REVERT: D 733 LEU cc_start: 0.8189 (tp) cc_final: 0.7701 (tp) outliers start: 1 outliers final: 0 residues processed: 491 average time/residue: 0.2069 time to fit residues: 169.5442 Evaluate side-chains 354 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 376 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 349 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 396 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 253 HIS ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.077056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059621 restraints weight = 163911.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061457 restraints weight = 89491.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.062704 restraints weight = 57479.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.063550 restraints weight = 41142.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.064107 restraints weight = 32153.562| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35481 Z= 0.205 Angle : 0.735 13.118 48144 Z= 0.382 Chirality : 0.047 0.377 5616 Planarity : 0.004 0.047 5961 Dihedral : 4.830 28.312 4659 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.03 % Allowed : 0.71 % Favored : 99.26 % 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: -1.79 (0.13), residues: 4257 helix: 0.02 (0.12), residues: 1884 sheet: -1.53 (0.21), residues: 609 loop : -2.39 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 266 TYR 0.029 0.002 TYR A 477 PHE 0.032 0.003 PHE C 156 TRP 0.047 0.003 TRP E 647 HIS 0.006 0.001 HIS C 119 Details of bonding type rmsd covalent geometry : bond 0.00455 (35463) covalent geometry : angle 0.73390 (48108) SS BOND : bond 0.00608 ( 18) SS BOND : angle 1.55317 ( 36) hydrogen bonds : bond 0.04610 ( 1644) hydrogen bonds : angle 5.10253 ( 4401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 437 time to evaluate : 1.388 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: A 140 SER cc_start: 0.9407 (t) cc_final: 0.8979 (p) REVERT: A 164 PHE cc_start: 0.8621 (t80) cc_final: 0.8384 (t80) REVERT: A 261 TYR cc_start: 0.8617 (t80) cc_final: 0.8269 (t80) REVERT: A 380 ASP cc_start: 0.8453 (t0) cc_final: 0.7797 (m-30) REVERT: A 433 PHE cc_start: 0.8330 (p90) cc_final: 0.7396 (p90) REVERT: A 623 ASP cc_start: 0.8408 (m-30) cc_final: 0.7511 (t0) REVERT: B 35 MET cc_start: 0.9141 (mtp) cc_final: 0.8768 (ttm) REVERT: B 52 MET cc_start: 0.7266 (tpt) cc_final: 0.6839 (tpt) REVERT: B 110 ASP cc_start: 0.8700 (m-30) cc_final: 0.8360 (m-30) REVERT: B 133 THR cc_start: 0.9473 (m) cc_final: 0.9129 (m) REVERT: B 239 GLN cc_start: 0.8958 (mt0) cc_final: 0.8583 (tt0) REVERT: B 308 TYR cc_start: 0.9107 (m-80) cc_final: 0.8189 (m-80) REVERT: B 491 LEU cc_start: 0.9479 (mt) cc_final: 0.8919 (tt) REVERT: B 501 LYS cc_start: 0.8850 (tptp) cc_final: 0.8626 (mmmt) REVERT: B 520 GLU cc_start: 0.8863 (tt0) cc_final: 0.8507 (tt0) REVERT: B 555 LEU cc_start: 0.8528 (mt) cc_final: 0.8307 (mt) REVERT: B 733 LEU cc_start: 0.8359 (tp) cc_final: 0.7759 (tp) REVERT: E 36 LEU cc_start: 0.9581 (tt) cc_final: 0.9316 (tp) REVERT: E 52 MET cc_start: 0.7934 (tpt) cc_final: 0.7726 (tpt) REVERT: E 140 SER cc_start: 0.9455 (t) cc_final: 0.9108 (p) REVERT: E 236 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8290 (mt-10) REVERT: E 323 SER cc_start: 0.8807 (m) cc_final: 0.8208 (t) REVERT: E 433 PHE cc_start: 0.8427 (p90) cc_final: 0.7495 (p90) REVERT: E 526 ASN cc_start: 0.9154 (m-40) cc_final: 0.8666 (p0) REVERT: E 623 ASP cc_start: 0.8045 (m-30) cc_final: 0.7398 (t0) REVERT: E 635 PHE cc_start: 0.7582 (t80) cc_final: 0.7338 (t80) REVERT: E 691 ASP cc_start: 0.8335 (t0) cc_final: 0.8037 (t0) REVERT: F 35 MET cc_start: 0.8844 (ttm) cc_final: 0.8493 (ttt) REVERT: F 52 MET cc_start: 0.7102 (tpp) cc_final: 0.6581 (tpp) REVERT: F 166 SER cc_start: 0.8221 (t) cc_final: 0.7835 (m) REVERT: F 308 TYR cc_start: 0.9038 (m-10) cc_final: 0.8392 (m-80) REVERT: F 473 GLU cc_start: 0.8328 (tt0) cc_final: 0.8053 (tt0) REVERT: F 496 ARG cc_start: 0.8035 (mmt-90) cc_final: 0.7332 (mmm160) REVERT: F 546 LEU cc_start: 0.9568 (tp) cc_final: 0.9300 (tp) REVERT: F 555 LEU cc_start: 0.8543 (mt) cc_final: 0.8156 (pp) REVERT: F 673 LYS cc_start: 0.9235 (mttt) cc_final: 0.8967 (pttm) REVERT: F 733 LEU cc_start: 0.8324 (tp) cc_final: 0.7894 (tp) REVERT: C 36 LEU cc_start: 0.9510 (tt) cc_final: 0.9172 (tp) REVERT: C 99 TYR cc_start: 0.7101 (m-80) cc_final: 0.6522 (m-80) REVERT: C 140 SER cc_start: 0.9334 (t) cc_final: 0.8965 (p) REVERT: C 265 MET cc_start: 0.9045 (mmm) cc_final: 0.8823 (mmt) REVERT: C 433 PHE cc_start: 0.8506 (p90) cc_final: 0.7717 (p90) REVERT: C 434 MET cc_start: 0.7580 (mmp) cc_final: 0.7180 (mmp) REVERT: C 471 LEU cc_start: 0.9368 (tp) cc_final: 0.9084 (tt) REVERT: C 526 ASN cc_start: 0.9187 (m-40) cc_final: 0.8168 (p0) REVERT: C 600 ARG cc_start: 0.8413 (tmt170) cc_final: 0.8178 (tpt90) REVERT: C 623 ASP cc_start: 0.8314 (m-30) cc_final: 0.7651 (t0) REVERT: C 691 ASP cc_start: 0.8540 (t0) cc_final: 0.8301 (t0) REVERT: D 28 THR cc_start: 0.9100 (m) cc_final: 0.8632 (t) REVERT: D 239 GLN cc_start: 0.8895 (mt0) cc_final: 0.8499 (pt0) REVERT: D 337 MET cc_start: 0.8667 (mmm) cc_final: 0.8119 (tmm) REVERT: D 375 MET cc_start: 0.8053 (ptp) cc_final: 0.7500 (ptp) REVERT: D 473 GLU cc_start: 0.8381 (tt0) cc_final: 0.8052 (tt0) REVERT: D 491 LEU cc_start: 0.9445 (tp) cc_final: 0.8917 (tp) REVERT: D 546 LEU cc_start: 0.9633 (tp) cc_final: 0.9416 (tp) REVERT: D 733 LEU cc_start: 0.8378 (tp) cc_final: 0.7878 (tp) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 0.2029 time to fit residues: 148.7339 Evaluate side-chains 324 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 184 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 258 optimal weight: 0.7980 chunk 402 optimal weight: 4.9990 chunk 132 optimal weight: 0.0980 chunk 269 optimal weight: 6.9990 chunk 401 optimal weight: 8.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS C 663 ASN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.079484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.062232 restraints weight = 162040.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064153 restraints weight = 87541.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065458 restraints weight = 55464.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066340 restraints weight = 39331.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066918 restraints weight = 30500.301| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35481 Z= 0.126 Angle : 0.679 16.214 48144 Z= 0.348 Chirality : 0.046 0.280 5616 Planarity : 0.004 0.046 5961 Dihedral : 4.690 26.843 4659 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.05 % Allowed : 0.26 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 4257 helix: 0.16 (0.12), residues: 1890 sheet: -1.52 (0.21), residues: 609 loop : -2.30 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 666 TYR 0.040 0.002 TYR E 477 PHE 0.033 0.002 PHE A 611 TRP 0.038 0.002 TRP E 647 HIS 0.007 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00269 (35463) covalent geometry : angle 0.67843 (48108) SS BOND : bond 0.00421 ( 18) SS BOND : angle 1.33301 ( 36) hydrogen bonds : bond 0.04122 ( 1644) hydrogen bonds : angle 4.86837 ( 4401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8514 Ramachandran restraints generated. 4257 Oldfield, 0 Emsley, 4257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 457 time to evaluate : 1.030 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.9025 (mtp) cc_final: 0.8532 (mtm) REVERT: A 36 LEU cc_start: 0.9543 (tt) cc_final: 0.9155 (tp) REVERT: A 140 SER cc_start: 0.9320 (t) cc_final: 0.8851 (p) REVERT: A 164 PHE cc_start: 0.8591 (t80) cc_final: 0.8313 (t80) REVERT: A 261 TYR cc_start: 0.8442 (t80) cc_final: 0.8159 (t80) REVERT: A 433 PHE cc_start: 0.8385 (p90) cc_final: 0.7633 (p90) REVERT: A 434 MET cc_start: 0.7080 (mmm) cc_final: 0.6589 (mmp) REVERT: A 526 ASN cc_start: 0.9327 (m-40) cc_final: 0.8315 (p0) REVERT: A 623 ASP cc_start: 0.8241 (m-30) cc_final: 0.7398 (t0) REVERT: A 691 ASP cc_start: 0.8403 (t0) cc_final: 0.8129 (t0) REVERT: B 52 MET cc_start: 0.7087 (tpt) cc_final: 0.5928 (tpt) REVERT: B 239 GLN cc_start: 0.8822 (mt0) cc_final: 0.8577 (tt0) REVERT: B 265 MET cc_start: 0.8496 (mmm) cc_final: 0.7384 (tpp) REVERT: B 308 TYR cc_start: 0.9039 (m-80) cc_final: 0.8169 (m-80) REVERT: B 324 PHE cc_start: 0.9264 (t80) cc_final: 0.9062 (t80) REVERT: B 491 LEU cc_start: 0.9443 (mt) cc_final: 0.8903 (tt) REVERT: B 520 GLU cc_start: 0.8783 (tt0) cc_final: 0.8410 (tt0) REVERT: B 555 LEU cc_start: 0.8569 (mt) cc_final: 0.8195 (pp) REVERT: B 733 LEU cc_start: 0.8291 (tp) cc_final: 0.7741 (tp) REVERT: E 36 LEU cc_start: 0.9586 (tt) cc_final: 0.9310 (tp) REVERT: E 140 SER cc_start: 0.9414 (t) cc_final: 0.9032 (p) REVERT: E 236 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8277 (mt-10) REVERT: E 323 SER cc_start: 0.8821 (m) cc_final: 0.8193 (t) REVERT: E 375 MET cc_start: 0.9366 (ptp) cc_final: 0.9028 (ptp) REVERT: E 433 PHE cc_start: 0.8522 (p90) cc_final: 0.7695 (p90) REVERT: E 434 MET cc_start: 0.7018 (mmp) cc_final: 0.6532 (mmp) REVERT: E 526 ASN cc_start: 0.9102 (m-40) cc_final: 0.8642 (p0) REVERT: E 623 ASP cc_start: 0.8118 (m-30) cc_final: 0.7402 (t0) REVERT: E 635 PHE cc_start: 0.7363 (t80) cc_final: 0.7153 (t80) REVERT: E 691 ASP cc_start: 0.8282 (t0) cc_final: 0.8030 (t0) REVERT: F 35 MET cc_start: 0.8767 (ttm) cc_final: 0.8285 (ttt) REVERT: F 52 MET cc_start: 0.6895 (tpp) cc_final: 0.6536 (tpp) REVERT: F 166 SER cc_start: 0.8079 (t) cc_final: 0.7706 (m) REVERT: F 308 TYR cc_start: 0.9049 (m-10) cc_final: 0.8379 (m-80) REVERT: F 445 LEU cc_start: 0.8966 (mm) cc_final: 0.8756 (mm) REVERT: F 473 GLU cc_start: 0.8264 (tt0) cc_final: 0.8028 (tt0) REVERT: F 496 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.7346 (mmm160) REVERT: F 546 LEU cc_start: 0.9537 (tp) cc_final: 0.9282 (tp) REVERT: F 555 LEU cc_start: 0.8561 (mt) cc_final: 0.8171 (pp) REVERT: F 673 LYS cc_start: 0.9236 (mttt) cc_final: 0.8941 (pttm) REVERT: F 733 LEU cc_start: 0.8278 (tp) cc_final: 0.7853 (tp) REVERT: C 36 LEU cc_start: 0.9480 (tt) cc_final: 0.9126 (tp) REVERT: C 52 MET cc_start: 0.8626 (mmm) cc_final: 0.7753 (mmm) REVERT: C 140 SER cc_start: 0.9264 (t) cc_final: 0.8892 (p) REVERT: C 265 MET cc_start: 0.9007 (mmm) cc_final: 0.8104 (mmm) REVERT: C 337 MET cc_start: 0.8870 (mmp) cc_final: 0.7591 (tmm) REVERT: C 471 LEU cc_start: 0.9350 (tp) cc_final: 0.9063 (tt) REVERT: C 623 ASP cc_start: 0.8243 (m-30) cc_final: 0.7543 (t0) REVERT: C 651 ILE cc_start: 0.9419 (pt) cc_final: 0.9161 (tp) REVERT: C 691 ASP cc_start: 0.8337 (t0) cc_final: 0.8136 (t0) REVERT: D 28 THR cc_start: 0.9089 (m) cc_final: 0.8625 (t) REVERT: D 52 MET cc_start: 0.6908 (tpp) cc_final: 0.5547 (tpp) REVERT: D 239 GLN cc_start: 0.8911 (mt0) cc_final: 0.8510 (pt0) REVERT: D 308 TYR cc_start: 0.9153 (m-80) cc_final: 0.8880 (m-80) REVERT: D 337 MET cc_start: 0.8675 (mmm) cc_final: 0.8049 (tmm) REVERT: D 375 MET cc_start: 0.7884 (ptp) cc_final: 0.7298 (ptp) REVERT: D 733 LEU cc_start: 0.8247 (tp) cc_final: 0.7764 (tp) outliers start: 2 outliers final: 0 residues processed: 459 average time/residue: 0.1957 time to fit residues: 152.3460 Evaluate side-chains 340 residues out of total 3999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 11 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 393 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 378 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN C 49 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.076591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.059182 restraints weight = 164190.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061018 restraints weight = 89378.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.062271 restraints weight = 57288.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.063114 restraints weight = 41009.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.063700 restraints weight = 31984.664| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35481 Z= 0.202 Angle : 0.721 14.854 48144 Z= 0.375 Chirality : 0.047 0.336 5616 Planarity : 0.004 0.047 5961 Dihedral : 4.854 28.485 4659 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.05 % Allowed : 0.37 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.13), residues: 4257 helix: 0.10 (0.12), residues: 1872 sheet: -1.62 (0.21), residues: 627 loop : -2.31 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 666 TYR 0.031 0.002 TYR B 534 PHE 0.035 0.003 PHE A 635 TRP 0.041 0.002 TRP E 647 HIS 0.009 0.001 HIS A 568 Details of bonding type rmsd covalent geometry : bond 0.00451 (35463) covalent geometry : angle 0.71978 (48108) SS BOND : bond 0.00592 ( 18) SS BOND : angle 1.42115 ( 36) hydrogen bonds : bond 0.04473 ( 1644) hydrogen bonds : angle 5.05924 ( 4401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6139.79 seconds wall clock time: 106 minutes 55.18 seconds (6415.18 seconds total)