Starting phenix.real_space_refine on Wed Mar 4 02:31:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wl2_32574/03_2026/7wl2_32574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wl2_32574/03_2026/7wl2_32574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wl2_32574/03_2026/7wl2_32574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wl2_32574/03_2026/7wl2_32574.map" model { file = "/net/cci-nas-00/data/ceres_data/7wl2_32574/03_2026/7wl2_32574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wl2_32574/03_2026/7wl2_32574.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 42 5.16 5 C 6656 2.51 5 N 1684 2.21 5 O 1816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 2.45, per 1000 atoms: 0.24 Number of scatterers: 10198 At special positions: 0 Unit cell: (86.818, 128.658, 116.106, 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 42 16.00 O 1816 8.00 N 1684 7.00 C 6656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 594.3 milliseconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 66.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.725A pdb=" N CYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.875A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.928A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 removed outlier: 5.005A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.877A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.675A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.865A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 216 through 240 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.505A pdb=" N TYR A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.514A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.807A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.568A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.800A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.588A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.646A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.865A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 670 through 685 removed outlier: 3.670A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.852A pdb=" N LYS A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.570A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.515A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.722A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.652A pdb=" N VAL B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.932A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 106 removed outlier: 3.809A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 removed outlier: 3.578A pdb=" N ALA B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.893A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 156 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.557A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 206 removed outlier: 4.062A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.789A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.529A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.658A pdb=" N THR B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 375 removed outlier: 3.719A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.613A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.798A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.503A pdb=" N ALA B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 446 through 457 removed outlier: 3.785A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.685A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.693A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 removed outlier: 3.501A pdb=" N LYS B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.787A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 3.571A pdb=" N VAL B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 676 " --> pdb=" O GLY B 672 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 4.041A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.573A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.503A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 734 " --> pdb=" O GLN B 730 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 735 " --> pdb=" O ASN B 731 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.781A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 22 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 removed outlier: 4.128A pdb=" N VAL A 163 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 175 " --> pdb=" O VAL A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.510A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 163 through 164 removed outlier: 4.191A pdb=" N VAL B 163 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR B 175 " --> pdb=" O VAL B 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA9, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.508A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1671 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: 1.67 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3214 1.34 - 1.46: 2202 1.46 - 1.58: 4920 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" CA VAL A 163 " pdb=" CB VAL A 163 " ideal model delta sigma weight residual 1.540 1.527 0.013 7.70e-03 1.69e+04 2.75e+00 bond pdb=" CA VAL B 163 " pdb=" CB VAL B 163 " ideal model delta sigma weight residual 1.541 1.526 0.015 1.24e-02 6.50e+03 1.44e+00 bond pdb=" C VAL A 163 " pdb=" O VAL A 163 " ideal model delta sigma weight residual 1.232 1.242 -0.009 8.90e-03 1.26e+04 1.12e+00 bond pdb=" CA THR A 45 " pdb=" CB THR A 45 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.92e-01 bond pdb=" CA THR B 45 " pdb=" CB THR B 45 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.79e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 13665 1.12 - 2.25: 368 2.25 - 3.37: 75 3.37 - 4.49: 11 4.49 - 5.62: 17 Bond angle restraints: 14136 Sorted by residual: angle pdb=" N PHE B 128 " pdb=" CA PHE B 128 " pdb=" C PHE B 128 " ideal model delta sigma weight residual 114.56 109.13 5.43 1.27e+00 6.20e-01 1.83e+01 angle pdb=" N VAL A 699 " pdb=" CA VAL A 699 " pdb=" C VAL A 699 " ideal model delta sigma weight residual 111.81 108.76 3.05 8.60e-01 1.35e+00 1.26e+01 angle pdb=" N VAL B 699 " pdb=" CA VAL B 699 " pdb=" C VAL B 699 " ideal model delta sigma weight residual 111.81 109.10 2.71 8.60e-01 1.35e+00 9.89e+00 angle pdb=" N ILE B 686 " pdb=" CA ILE B 686 " pdb=" C ILE B 686 " ideal model delta sigma weight residual 111.77 109.05 2.72 1.04e+00 9.25e-01 6.84e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.68 -4.71 1.80e+00 3.09e-01 6.83e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 5961 16.59 - 33.18: 182 33.18 - 49.77: 28 49.77 - 66.36: 8 66.36 - 82.95: 3 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" CA ASP A 669 " pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" N MET B 488 " pdb=" CA MET B 488 " pdb=" CB MET B 488 " pdb=" CG MET B 488 " ideal model delta sinusoidal sigma weight residual -180.00 -121.83 -58.17 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LYS A 681 " pdb=" CA LYS A 681 " pdb=" CB LYS A 681 " pdb=" CG LYS A 681 " ideal model delta sinusoidal sigma weight residual -180.00 -122.73 -57.27 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 998 0.026 - 0.051: 405 0.051 - 0.077: 217 0.077 - 0.102: 79 0.102 - 0.128: 19 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA ILE B 300 " pdb=" N ILE B 300 " pdb=" C ILE B 300 " pdb=" CB ILE B 300 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE A 300 " pdb=" N ILE A 300 " pdb=" C ILE A 300 " pdb=" CB ILE A 300 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 553 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 553 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO A 112 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.018 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1140 2.75 - 3.28: 10835 3.28 - 3.82: 16534 3.82 - 4.36: 19706 4.36 - 4.90: 33830 Nonbonded interactions: 82045 Sorted by model distance: nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.207 3.040 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.231 3.040 nonbonded pdb=" O TYR A 247 " pdb=" OG SER A 252 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR B 118 " pdb=" O GLY B 334 " model vdw 2.277 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.282 3.120 ... (remaining 82040 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.770 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 : 0.002 0.021 10400 Z= 0.108 Angle : 0.490 5.616 14136 Z= 0.302 Chirality : 0.037 0.128 1718 Planarity : 0.003 0.036 1758 Dihedral : 8.514 82.947 3710 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 2.14 % Allowed : 5.61 % Favored : 92.25 % 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: -4.09 (0.19), residues: 1322 helix: -2.28 (0.14), residues: 854 sheet: -3.88 (0.57), residues: 36 loop : -3.19 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 512 TYR 0.007 0.001 TYR A 377 PHE 0.009 0.001 PHE B 555 TRP 0.003 0.000 TRP A 83 HIS 0.002 0.000 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00183 (10400) covalent geometry : angle 0.49015 (14136) hydrogen bonds : bond 0.23185 ( 573) hydrogen bonds : angle 7.01499 ( 1671) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 385 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASP cc_start: 0.6043 (OUTLIER) cc_final: 0.5719 (p0) REVERT: A 237 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8078 (ttpt) REVERT: A 254 ILE cc_start: 0.7961 (mm) cc_final: 0.7704 (mm) REVERT: A 369 LYS cc_start: 0.7682 (mmtt) cc_final: 0.7445 (mmtp) REVERT: A 377 TYR cc_start: 0.7118 (p90) cc_final: 0.6908 (p90) REVERT: A 384 GLU cc_start: 0.7180 (tp30) cc_final: 0.6581 (tp30) REVERT: A 385 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7054 (t80) REVERT: A 405 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8059 (p) REVERT: A 414 GLU cc_start: 0.6628 (tm-30) cc_final: 0.6342 (tm-30) REVERT: A 447 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7921 (ttmt) REVERT: A 448 SER cc_start: 0.8224 (p) cc_final: 0.7961 (p) REVERT: A 459 LYS cc_start: 0.7769 (tppp) cc_final: 0.7016 (tppp) REVERT: A 528 ASP cc_start: 0.8241 (p0) cc_final: 0.8040 (p0) REVERT: A 531 LYS cc_start: 0.8386 (mmmt) cc_final: 0.8050 (mmtt) REVERT: A 580 LYS cc_start: 0.6322 (ttpt) cc_final: 0.5759 (tmtt) REVERT: A 652 LYS cc_start: 0.5140 (pttt) cc_final: 0.4156 (pttt) REVERT: A 684 GLN cc_start: 0.8051 (tp40) cc_final: 0.7549 (tp-100) REVERT: A 687 ASP cc_start: 0.7271 (t70) cc_final: 0.6981 (t0) REVERT: A 717 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7943 (mtt90) REVERT: B 87 ASP cc_start: 0.6927 (m-30) cc_final: 0.6609 (m-30) REVERT: B 92 VAL cc_start: 0.8334 (m) cc_final: 0.8079 (t) REVERT: B 245 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7657 (ttmt) REVERT: B 255 TYR cc_start: 0.8269 (m-10) cc_final: 0.7878 (m-10) REVERT: B 289 ASN cc_start: 0.7756 (t0) cc_final: 0.7351 (t0) REVERT: B 303 GLU cc_start: 0.6944 (mp0) cc_final: 0.6667 (mp0) REVERT: B 384 GLU cc_start: 0.7820 (tp30) cc_final: 0.7546 (tp30) REVERT: B 385 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: B 447 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7846 (mtmm) REVERT: B 475 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7442 (t0) REVERT: B 478 ASP cc_start: 0.7298 (m-30) cc_final: 0.6603 (m-30) REVERT: B 492 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7924 (pp) REVERT: B 499 LEU cc_start: 0.8440 (tp) cc_final: 0.8175 (tp) REVERT: B 531 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7879 (mmtm) REVERT: B 538 ASN cc_start: 0.6687 (p0) cc_final: 0.6347 (p0) REVERT: B 563 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7969 (mmmt) REVERT: B 564 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7783 (ttmm) REVERT: B 580 LYS cc_start: 0.6744 (ttpt) cc_final: 0.6296 (tmtt) REVERT: B 669 ASP cc_start: 0.6822 (t0) cc_final: 0.6578 (t0) REVERT: B 681 LYS cc_start: 0.8007 (mptt) cc_final: 0.7654 (mptt) REVERT: B 682 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6861 (mm-30) REVERT: B 685 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7436 (mtm180) REVERT: B 687 ASP cc_start: 0.7193 (t70) cc_final: 0.6988 (t0) REVERT: B 714 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7271 (mtm-85) REVERT: B 732 GLN cc_start: 0.7006 (tm-30) cc_final: 0.6718 (tm-30) outliers start: 24 outliers final: 4 residues processed: 398 average time/residue: 0.1239 time to fit residues: 65.0801 Evaluate side-chains 325 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 315 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 475 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 475 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 673 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 135 HIS A 207 GLN A 262 GLN A 413 GLN A 475 ASN A 579 ASN A 656 HIS A 696 GLN B 101 GLN B 135 HIS B 413 GLN B 464 GLN B 475 ASN B 579 ASN B 656 HIS B 696 GLN B 731 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108681 restraints weight = 15715.486| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.22 r_work: 0.3292 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10400 Z= 0.204 Angle : 0.613 11.531 14136 Z= 0.321 Chirality : 0.044 0.215 1718 Planarity : 0.005 0.053 1758 Dihedral : 4.986 55.926 1432 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.30 % Allowed : 14.62 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.22), residues: 1322 helix: -0.51 (0.17), residues: 866 sheet: -3.32 (0.65), residues: 36 loop : -2.74 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 717 TYR 0.019 0.002 TYR B 377 PHE 0.026 0.002 PHE B 130 TRP 0.007 0.001 TRP B 482 HIS 0.010 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00448 (10400) covalent geometry : angle 0.61285 (14136) hydrogen bonds : bond 0.05063 ( 573) hydrogen bonds : angle 4.24113 ( 1671) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.7899 (mmt-90) REVERT: A 79 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.7174 (mmm160) REVERT: A 182 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6636 (p0) REVERT: A 235 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7820 (mm-40) REVERT: A 237 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8295 (ttpt) REVERT: A 247 TYR cc_start: 0.8297 (m-10) cc_final: 0.7350 (m-80) REVERT: A 287 GLU cc_start: 0.7624 (pp20) cc_final: 0.7165 (pp20) REVERT: A 291 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7551 (ttm170) REVERT: A 320 GLU cc_start: 0.7420 (tp30) cc_final: 0.7201 (tp30) REVERT: A 361 TYR cc_start: 0.8494 (t80) cc_final: 0.8010 (t80) REVERT: A 369 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7887 (mttp) REVERT: A 371 TYR cc_start: 0.8176 (m-80) cc_final: 0.7919 (m-80) REVERT: A 377 TYR cc_start: 0.7850 (p90) cc_final: 0.7538 (p90) REVERT: A 384 GLU cc_start: 0.7929 (tp30) cc_final: 0.7397 (tp30) REVERT: A 385 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7303 (t80) REVERT: A 432 MET cc_start: 0.8442 (tpt) cc_final: 0.7823 (tpt) REVERT: A 459 LYS cc_start: 0.8050 (tppp) cc_final: 0.7726 (tppp) REVERT: A 475 ASN cc_start: 0.8349 (t0) cc_final: 0.7888 (t0) REVERT: A 503 LEU cc_start: 0.8303 (mt) cc_final: 0.8097 (mm) REVERT: A 518 TRP cc_start: 0.8720 (p-90) cc_final: 0.8445 (p-90) REVERT: A 576 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7841 (ttm-80) REVERT: A 580 LYS cc_start: 0.6973 (ttpt) cc_final: 0.6587 (ttpt) REVERT: A 652 LYS cc_start: 0.5437 (pttt) cc_final: 0.3990 (pttt) REVERT: A 669 ASP cc_start: 0.6885 (t0) cc_final: 0.6653 (t0) REVERT: A 677 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7821 (ttp80) REVERT: A 681 LYS cc_start: 0.8095 (mptt) cc_final: 0.7794 (mptt) REVERT: A 684 GLN cc_start: 0.8333 (tp40) cc_final: 0.8071 (tp-100) REVERT: A 687 ASP cc_start: 0.7960 (t70) cc_final: 0.7635 (t0) REVERT: B 39 ARG cc_start: 0.8053 (tpp80) cc_final: 0.7648 (tpp-160) REVERT: B 137 SER cc_start: 0.8432 (p) cc_final: 0.8174 (t) REVERT: B 155 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8000 (mtm) REVERT: B 245 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8113 (ttmt) REVERT: B 255 TYR cc_start: 0.8818 (m-10) cc_final: 0.8104 (m-80) REVERT: B 289 ASN cc_start: 0.8366 (t0) cc_final: 0.8038 (t0) REVERT: B 309 ILE cc_start: 0.8750 (tt) cc_final: 0.8519 (pt) REVERT: B 320 GLU cc_start: 0.7447 (tp30) cc_final: 0.7214 (tp30) REVERT: B 361 TYR cc_start: 0.8504 (t80) cc_final: 0.7778 (t80) REVERT: B 384 GLU cc_start: 0.8157 (tp30) cc_final: 0.7905 (tp30) REVERT: B 385 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: B 459 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7759 (tppp) REVERT: B 462 PHE cc_start: 0.8260 (m-10) cc_final: 0.7979 (m-10) REVERT: B 475 ASN cc_start: 0.8446 (t0) cc_final: 0.8189 (t0) REVERT: B 492 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8372 (pt) REVERT: B 538 ASN cc_start: 0.7456 (p0) cc_final: 0.7121 (p0) REVERT: B 560 ASP cc_start: 0.8049 (m-30) cc_final: 0.7826 (m-30) REVERT: B 564 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8268 (ttmm) REVERT: B 580 LYS cc_start: 0.7244 (ttpt) cc_final: 0.6852 (tmtt) REVERT: B 681 LYS cc_start: 0.8531 (mptt) cc_final: 0.8234 (mptt) REVERT: B 682 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 687 ASP cc_start: 0.7999 (t70) cc_final: 0.7794 (t0) outliers start: 37 outliers final: 22 residues processed: 334 average time/residue: 0.1173 time to fit residues: 52.1340 Evaluate side-chains 327 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 69 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN B 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106041 restraints weight = 15800.713| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.24 r_work: 0.3247 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10400 Z= 0.220 Angle : 0.607 10.238 14136 Z= 0.320 Chirality : 0.044 0.165 1718 Planarity : 0.005 0.058 1758 Dihedral : 5.011 58.705 1426 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.03 % Favored : 92.89 % Rotamer: Outliers : 4.99 % Allowed : 15.69 % Favored : 79.32 % 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: -1.08 (0.23), residues: 1322 helix: 0.15 (0.18), residues: 854 sheet: -2.72 (0.71), residues: 36 loop : -2.22 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 677 TYR 0.021 0.002 TYR B 377 PHE 0.013 0.002 PHE A 562 TRP 0.009 0.001 TRP B 482 HIS 0.003 0.001 HIS B 656 Details of bonding type rmsd covalent geometry : bond 0.00489 (10400) covalent geometry : angle 0.60745 (14136) hydrogen bonds : bond 0.04838 ( 573) hydrogen bonds : angle 4.03073 ( 1671) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 36 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.7869 (mmt-90) REVERT: A 79 ARG cc_start: 0.7587 (mtt-85) cc_final: 0.7323 (mmm-85) REVERT: A 182 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6807 (p0) REVERT: A 235 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7956 (mm-40) REVERT: A 237 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8393 (ttpt) REVERT: A 287 GLU cc_start: 0.7654 (pp20) cc_final: 0.7211 (pp20) REVERT: A 320 GLU cc_start: 0.7539 (tp30) cc_final: 0.7307 (tp30) REVERT: A 369 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7984 (mttp) REVERT: A 370 VAL cc_start: 0.8451 (t) cc_final: 0.8154 (t) REVERT: A 377 TYR cc_start: 0.8075 (p90) cc_final: 0.7864 (p90) REVERT: A 384 GLU cc_start: 0.8065 (tp30) cc_final: 0.7569 (tp30) REVERT: A 385 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 459 LYS cc_start: 0.8082 (tppp) cc_final: 0.7753 (tppp) REVERT: A 475 ASN cc_start: 0.8325 (t0) cc_final: 0.7787 (t0) REVERT: A 478 ASP cc_start: 0.7904 (m-30) cc_final: 0.7411 (m-30) REVERT: A 538 ASN cc_start: 0.7680 (p0) cc_final: 0.7323 (p0) REVERT: A 576 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7828 (ttm-80) REVERT: A 580 LYS cc_start: 0.6947 (ttpt) cc_final: 0.6556 (ttpt) REVERT: A 669 ASP cc_start: 0.6905 (t0) cc_final: 0.6687 (t0) REVERT: A 677 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7714 (ttp80) REVERT: A 681 LYS cc_start: 0.8080 (mptt) cc_final: 0.7748 (mptt) REVERT: A 684 GLN cc_start: 0.8350 (tp40) cc_final: 0.8091 (tp-100) REVERT: A 687 ASP cc_start: 0.7995 (t70) cc_final: 0.7631 (t0) REVERT: A 730 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: B 21 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8112 (p) REVERT: B 39 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7618 (tpp-160) REVERT: B 245 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8083 (ttmt) REVERT: B 255 TYR cc_start: 0.8808 (m-10) cc_final: 0.8011 (m-80) REVERT: B 259 GLU cc_start: 0.8309 (tt0) cc_final: 0.8106 (tt0) REVERT: B 289 ASN cc_start: 0.8359 (t0) cc_final: 0.8025 (t0) REVERT: B 320 GLU cc_start: 0.7717 (tp30) cc_final: 0.7457 (tp30) REVERT: B 361 TYR cc_start: 0.8479 (t80) cc_final: 0.7646 (t80) REVERT: B 370 VAL cc_start: 0.8564 (t) cc_final: 0.8307 (t) REVERT: B 384 GLU cc_start: 0.8138 (tp30) cc_final: 0.7853 (tp30) REVERT: B 385 PHE cc_start: 0.8689 (m-80) cc_final: 0.7714 (m-80) REVERT: B 459 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7794 (tppp) REVERT: B 462 PHE cc_start: 0.8334 (m-10) cc_final: 0.8052 (m-10) REVERT: B 475 ASN cc_start: 0.8405 (t0) cc_final: 0.8087 (t0) REVERT: B 492 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8401 (pt) REVERT: B 538 ASN cc_start: 0.7614 (p0) cc_final: 0.7236 (p0) REVERT: B 560 ASP cc_start: 0.8095 (m-30) cc_final: 0.7794 (m-30) REVERT: B 576 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7776 (mtt90) REVERT: B 587 ARG cc_start: 0.6141 (tpp-160) cc_final: 0.5657 (tpp-160) REVERT: B 681 LYS cc_start: 0.8462 (mptt) cc_final: 0.8176 (mptt) REVERT: B 682 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 687 ASP cc_start: 0.7993 (t70) cc_final: 0.7705 (t70) outliers start: 56 outliers final: 38 residues processed: 339 average time/residue: 0.1252 time to fit residues: 55.7886 Evaluate side-chains 346 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 77 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 79 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 HIS B 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106561 restraints weight = 15708.591| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.24 r_work: 0.3256 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10400 Z= 0.176 Angle : 0.570 7.998 14136 Z= 0.302 Chirality : 0.043 0.149 1718 Planarity : 0.004 0.054 1758 Dihedral : 4.854 56.587 1424 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 4.81 % Allowed : 16.49 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1322 helix: 0.44 (0.18), residues: 872 sheet: -1.95 (0.79), residues: 36 loop : -2.17 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.016 0.001 TYR B 377 PHE 0.013 0.001 PHE A 115 TRP 0.009 0.001 TRP B 482 HIS 0.003 0.001 HIS A 656 Details of bonding type rmsd covalent geometry : bond 0.00390 (10400) covalent geometry : angle 0.57014 (14136) hydrogen bonds : bond 0.04386 ( 573) hydrogen bonds : angle 3.86844 ( 1671) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 303 time to evaluate : 0.379 Fit side-chains REVERT: A 21 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 79 ARG cc_start: 0.7528 (mtt-85) cc_final: 0.7252 (mmm-85) REVERT: A 182 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6853 (p0) REVERT: A 235 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7925 (mm-40) REVERT: A 287 GLU cc_start: 0.7641 (pp20) cc_final: 0.7191 (pp20) REVERT: A 361 TYR cc_start: 0.8475 (t80) cc_final: 0.7887 (t80) REVERT: A 369 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7977 (mttp) REVERT: A 370 VAL cc_start: 0.8460 (t) cc_final: 0.8205 (t) REVERT: A 377 TYR cc_start: 0.8091 (p90) cc_final: 0.7884 (p90) REVERT: A 384 GLU cc_start: 0.8046 (tp30) cc_final: 0.7555 (tp30) REVERT: A 385 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7862 (m-10) REVERT: A 475 ASN cc_start: 0.8242 (t0) cc_final: 0.8036 (t0) REVERT: A 538 ASN cc_start: 0.7718 (p0) cc_final: 0.7263 (p0) REVERT: A 546 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8253 (mtpp) REVERT: A 564 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8156 (ttmm) REVERT: A 576 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7818 (ttm-80) REVERT: A 580 LYS cc_start: 0.7016 (ttpt) cc_final: 0.6582 (ttpt) REVERT: A 669 ASP cc_start: 0.6883 (t0) cc_final: 0.6641 (t0) REVERT: A 677 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7676 (ttp80) REVERT: A 681 LYS cc_start: 0.8050 (mptt) cc_final: 0.7729 (mptt) REVERT: A 684 GLN cc_start: 0.8326 (tp40) cc_final: 0.8080 (tp40) REVERT: A 687 ASP cc_start: 0.7972 (t70) cc_final: 0.7577 (t0) REVERT: A 730 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: B 21 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 245 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8159 (ttmt) REVERT: B 255 TYR cc_start: 0.8790 (m-10) cc_final: 0.8041 (m-10) REVERT: B 289 ASN cc_start: 0.8332 (t0) cc_final: 0.7997 (t0) REVERT: B 320 GLU cc_start: 0.7736 (tp30) cc_final: 0.7509 (tp30) REVERT: B 361 TYR cc_start: 0.8447 (t80) cc_final: 0.7587 (t80) REVERT: B 370 VAL cc_start: 0.8546 (t) cc_final: 0.8292 (t) REVERT: B 384 GLU cc_start: 0.8126 (tp30) cc_final: 0.7822 (tp30) REVERT: B 385 PHE cc_start: 0.8639 (m-80) cc_final: 0.7678 (m-80) REVERT: B 459 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7783 (tppp) REVERT: B 462 PHE cc_start: 0.8333 (m-10) cc_final: 0.7984 (m-10) REVERT: B 475 ASN cc_start: 0.8404 (t0) cc_final: 0.8159 (t0) REVERT: B 492 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8422 (pt) REVERT: B 538 ASN cc_start: 0.7609 (p0) cc_final: 0.7214 (p0) REVERT: B 560 ASP cc_start: 0.8065 (m-30) cc_final: 0.7767 (m-30) REVERT: B 573 ASP cc_start: 0.7717 (t70) cc_final: 0.7358 (t0) REVERT: B 576 ARG cc_start: 0.8048 (mtt90) cc_final: 0.7470 (ttm110) REVERT: B 652 LYS cc_start: 0.6067 (pttt) cc_final: 0.5792 (pttt) REVERT: B 681 LYS cc_start: 0.8408 (mptt) cc_final: 0.8138 (mptt) REVERT: B 685 ARG cc_start: 0.8506 (mtm180) cc_final: 0.8179 (mtm180) REVERT: B 687 ASP cc_start: 0.7994 (t70) cc_final: 0.7672 (t70) outliers start: 54 outliers final: 37 residues processed: 331 average time/residue: 0.1231 time to fit residues: 53.9181 Evaluate side-chains 335 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 291 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 76 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 119 optimal weight: 0.0870 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107473 restraints weight = 15639.202| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.24 r_work: 0.3270 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10400 Z= 0.138 Angle : 0.552 6.838 14136 Z= 0.293 Chirality : 0.042 0.150 1718 Planarity : 0.004 0.049 1758 Dihedral : 4.814 56.620 1424 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 5.35 % Allowed : 16.31 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1322 helix: 0.63 (0.18), residues: 878 sheet: -1.43 (0.85), residues: 36 loop : -2.04 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.015 0.001 TYR B 377 PHE 0.019 0.001 PHE A 130 TRP 0.009 0.001 TRP B 482 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00301 (10400) covalent geometry : angle 0.55174 (14136) hydrogen bonds : bond 0.04064 ( 573) hydrogen bonds : angle 3.74229 ( 1671) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 309 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8212 (p) REVERT: A 79 ARG cc_start: 0.7512 (mtt-85) cc_final: 0.7241 (mmm-85) REVERT: A 182 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6850 (p0) REVERT: A 235 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7875 (mm-40) REVERT: A 287 GLU cc_start: 0.7663 (pp20) cc_final: 0.7241 (pp20) REVERT: A 369 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7967 (mttp) REVERT: A 370 VAL cc_start: 0.8483 (t) cc_final: 0.8226 (t) REVERT: A 384 GLU cc_start: 0.8030 (tp30) cc_final: 0.7537 (tp30) REVERT: A 475 ASN cc_start: 0.8235 (t0) cc_final: 0.7992 (t0) REVERT: A 538 ASN cc_start: 0.7757 (p0) cc_final: 0.7305 (p0) REVERT: A 546 LYS cc_start: 0.8406 (mmtm) cc_final: 0.8194 (mmmm) REVERT: A 564 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8102 (ttmm) REVERT: A 576 ARG cc_start: 0.8072 (mtt90) cc_final: 0.7765 (ttm-80) REVERT: A 580 LYS cc_start: 0.7001 (ttpt) cc_final: 0.6562 (ttpt) REVERT: A 677 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7639 (ttp80) REVERT: A 681 LYS cc_start: 0.8066 (mptt) cc_final: 0.7745 (mptt) REVERT: A 684 GLN cc_start: 0.8333 (tp40) cc_final: 0.8006 (tp40) REVERT: A 687 ASP cc_start: 0.7929 (t70) cc_final: 0.7568 (t0) REVERT: A 696 GLN cc_start: 0.7404 (mt0) cc_final: 0.7020 (mt0) REVERT: A 727 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7816 (mm) REVERT: A 730 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: B 21 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8168 (p) REVERT: B 39 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7629 (tpp-160) REVERT: B 79 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7267 (ttm170) REVERT: B 237 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8455 (mtpp) REVERT: B 245 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8115 (ttmt) REVERT: B 255 TYR cc_start: 0.8794 (m-10) cc_final: 0.8069 (m-10) REVERT: B 276 LEU cc_start: 0.8577 (tt) cc_final: 0.8335 (tt) REVERT: B 289 ASN cc_start: 0.8264 (t0) cc_final: 0.7948 (t0) REVERT: B 323 TYR cc_start: 0.8653 (m-10) cc_final: 0.8446 (m-10) REVERT: B 361 TYR cc_start: 0.8433 (t80) cc_final: 0.7604 (t80) REVERT: B 370 VAL cc_start: 0.8517 (t) cc_final: 0.8272 (t) REVERT: B 384 GLU cc_start: 0.8123 (tp30) cc_final: 0.7811 (tp30) REVERT: B 385 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 414 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7209 (tm-30) REVERT: B 459 LYS cc_start: 0.8120 (tppp) cc_final: 0.7793 (tppp) REVERT: B 475 ASN cc_start: 0.8399 (t0) cc_final: 0.8111 (t0) REVERT: B 492 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8442 (pt) REVERT: B 528 ASP cc_start: 0.8607 (p0) cc_final: 0.8383 (p0) REVERT: B 538 ASN cc_start: 0.7608 (p0) cc_final: 0.7213 (p0) REVERT: B 560 ASP cc_start: 0.8088 (m-30) cc_final: 0.7796 (m-30) REVERT: B 573 ASP cc_start: 0.7692 (t70) cc_final: 0.7427 (t0) REVERT: B 576 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7658 (mtt90) REVERT: B 652 LYS cc_start: 0.5938 (pttt) cc_final: 0.5673 (pttt) REVERT: B 681 LYS cc_start: 0.8399 (mptt) cc_final: 0.8128 (mptt) REVERT: B 685 ARG cc_start: 0.8476 (mtm180) cc_final: 0.8163 (mtm180) REVERT: B 687 ASP cc_start: 0.7983 (t70) cc_final: 0.7685 (t70) outliers start: 60 outliers final: 42 residues processed: 340 average time/residue: 0.1318 time to fit residues: 58.8971 Evaluate side-chains 341 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 49 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106342 restraints weight = 15636.014| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.07 r_work: 0.3267 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10400 Z= 0.223 Angle : 0.608 7.229 14136 Z= 0.322 Chirality : 0.045 0.170 1718 Planarity : 0.004 0.055 1758 Dihedral : 4.974 55.211 1424 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 5.61 % Allowed : 16.58 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1322 helix: 0.60 (0.18), residues: 878 sheet: -1.27 (0.85), residues: 36 loop : -2.22 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 38 TYR 0.017 0.002 TYR A 377 PHE 0.019 0.002 PHE B 130 TRP 0.009 0.001 TRP B 482 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00500 (10400) covalent geometry : angle 0.60775 (14136) hydrogen bonds : bond 0.04630 ( 573) hydrogen bonds : angle 3.83347 ( 1671) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 297 time to evaluate : 0.355 Fit side-chains REVERT: A 21 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 66 LYS cc_start: 0.8378 (tptp) cc_final: 0.7965 (tptp) REVERT: A 79 ARG cc_start: 0.7586 (mtt-85) cc_final: 0.7315 (mmm-85) REVERT: A 182 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6893 (p0) REVERT: A 235 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7856 (mm-40) REVERT: A 287 GLU cc_start: 0.7710 (pp20) cc_final: 0.7266 (pp20) REVERT: A 369 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8088 (mttp) REVERT: A 384 GLU cc_start: 0.7963 (tp30) cc_final: 0.7550 (tp30) REVERT: A 385 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: A 538 ASN cc_start: 0.7865 (p0) cc_final: 0.7452 (p0) REVERT: A 546 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8182 (mmmm) REVERT: A 564 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8099 (ttmm) REVERT: A 677 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7704 (ttp80) REVERT: A 681 LYS cc_start: 0.8184 (mptt) cc_final: 0.7909 (mptt) REVERT: A 684 GLN cc_start: 0.8308 (tp40) cc_final: 0.8024 (tp40) REVERT: A 687 ASP cc_start: 0.7809 (t70) cc_final: 0.7491 (t0) REVERT: B 21 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 79 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7366 (ttm170) REVERT: B 245 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8239 (ttmt) REVERT: B 255 TYR cc_start: 0.8804 (m-10) cc_final: 0.8047 (m-10) REVERT: B 276 LEU cc_start: 0.8679 (tt) cc_final: 0.8447 (tt) REVERT: B 323 TYR cc_start: 0.8550 (m-10) cc_final: 0.8341 (m-10) REVERT: B 384 GLU cc_start: 0.8085 (tp30) cc_final: 0.7757 (tp30) REVERT: B 385 PHE cc_start: 0.8646 (m-80) cc_final: 0.8028 (m-80) REVERT: B 414 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7197 (tm-30) REVERT: B 459 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7838 (tppp) REVERT: B 475 ASN cc_start: 0.8268 (t0) cc_final: 0.8059 (t0) REVERT: B 492 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8484 (pt) REVERT: B 538 ASN cc_start: 0.7755 (p0) cc_final: 0.7393 (p0) REVERT: B 560 ASP cc_start: 0.8018 (m-30) cc_final: 0.7742 (m-30) REVERT: B 681 LYS cc_start: 0.8454 (mptt) cc_final: 0.8210 (mptt) REVERT: B 687 ASP cc_start: 0.7935 (t70) cc_final: 0.7649 (t70) outliers start: 63 outliers final: 49 residues processed: 326 average time/residue: 0.1252 time to fit residues: 53.7501 Evaluate side-chains 343 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 288 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN B 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106014 restraints weight = 15466.648| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.07 r_work: 0.3266 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10400 Z= 0.217 Angle : 0.620 13.368 14136 Z= 0.325 Chirality : 0.044 0.171 1718 Planarity : 0.004 0.054 1758 Dihedral : 5.010 53.869 1424 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.58 % Favored : 93.27 % Rotamer: Outliers : 4.99 % Allowed : 17.47 % Favored : 77.54 % 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: -0.29 (0.24), residues: 1322 helix: 0.69 (0.18), residues: 878 sheet: -0.92 (0.90), residues: 36 loop : -2.03 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.023 0.002 TYR A 377 PHE 0.023 0.002 PHE A 130 TRP 0.010 0.001 TRP B 482 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00484 (10400) covalent geometry : angle 0.62046 (14136) hydrogen bonds : bond 0.04590 ( 573) hydrogen bonds : angle 3.83537 ( 1671) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 296 time to evaluate : 0.366 Fit side-chains REVERT: A 21 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8241 (p) REVERT: A 66 LYS cc_start: 0.8343 (tptp) cc_final: 0.7931 (tptp) REVERT: A 235 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7844 (mm-40) REVERT: A 245 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8305 (ttmt) REVERT: A 247 TYR cc_start: 0.8227 (m-10) cc_final: 0.7074 (m-80) REVERT: A 287 GLU cc_start: 0.7687 (pp20) cc_final: 0.7245 (pp20) REVERT: A 369 LYS cc_start: 0.8336 (mmtt) cc_final: 0.8092 (mttp) REVERT: A 384 GLU cc_start: 0.7956 (tp30) cc_final: 0.7558 (tp30) REVERT: A 385 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: A 538 ASN cc_start: 0.7921 (p0) cc_final: 0.7610 (p0) REVERT: A 564 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8096 (ttmm) REVERT: A 677 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7691 (ttp80) REVERT: A 681 LYS cc_start: 0.8192 (mptt) cc_final: 0.7923 (mptt) REVERT: A 684 GLN cc_start: 0.8270 (tp40) cc_final: 0.8020 (tp40) REVERT: A 687 ASP cc_start: 0.7830 (t70) cc_final: 0.7515 (t0) REVERT: A 696 GLN cc_start: 0.7317 (mm-40) cc_final: 0.7069 (mm-40) REVERT: A 730 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: B 21 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 79 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7373 (ttm170) REVERT: B 245 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8119 (ttmt) REVERT: B 255 TYR cc_start: 0.8795 (m-10) cc_final: 0.8052 (m-10) REVERT: B 276 LEU cc_start: 0.8674 (tt) cc_final: 0.8447 (tt) REVERT: B 289 ASN cc_start: 0.8425 (t0) cc_final: 0.8109 (t0) REVERT: B 384 GLU cc_start: 0.8046 (tp30) cc_final: 0.7757 (tp30) REVERT: B 385 PHE cc_start: 0.8643 (m-80) cc_final: 0.8040 (m-80) REVERT: B 414 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 459 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7843 (tppp) REVERT: B 475 ASN cc_start: 0.8273 (t0) cc_final: 0.8044 (t0) REVERT: B 492 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8482 (pt) REVERT: B 538 ASN cc_start: 0.7875 (p0) cc_final: 0.7571 (p0) REVERT: B 560 ASP cc_start: 0.8014 (m-30) cc_final: 0.7757 (m-30) REVERT: B 681 LYS cc_start: 0.8409 (mptt) cc_final: 0.8173 (mptt) REVERT: B 687 ASP cc_start: 0.7918 (t70) cc_final: 0.7635 (t70) outliers start: 56 outliers final: 44 residues processed: 321 average time/residue: 0.1216 time to fit residues: 51.5083 Evaluate side-chains 340 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 229 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107572 restraints weight = 15419.189| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.07 r_work: 0.3271 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10400 Z= 0.163 Angle : 0.593 12.026 14136 Z= 0.311 Chirality : 0.043 0.171 1718 Planarity : 0.004 0.051 1758 Dihedral : 4.641 54.790 1421 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.05 % Favored : 93.80 % Rotamer: Outliers : 4.19 % Allowed : 18.98 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1322 helix: 0.74 (0.18), residues: 880 sheet: -0.61 (0.95), residues: 36 loop : -2.01 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.024 0.001 TYR A 377 PHE 0.023 0.001 PHE A 130 TRP 0.010 0.001 TRP B 482 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00364 (10400) covalent geometry : angle 0.59267 (14136) hydrogen bonds : bond 0.04273 ( 573) hydrogen bonds : angle 3.76128 ( 1671) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 129 VAL cc_start: 0.7812 (m) cc_final: 0.7463 (p) REVERT: A 235 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7712 (mm-40) REVERT: A 245 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8271 (ttmt) REVERT: A 272 PHE cc_start: 0.8561 (t80) cc_final: 0.8286 (t80) REVERT: A 287 GLU cc_start: 0.7652 (pp20) cc_final: 0.7220 (pp20) REVERT: A 369 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8068 (mttp) REVERT: A 370 VAL cc_start: 0.8636 (t) cc_final: 0.8361 (t) REVERT: A 384 GLU cc_start: 0.7947 (tp30) cc_final: 0.7537 (tp30) REVERT: A 385 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: A 538 ASN cc_start: 0.7904 (p0) cc_final: 0.7579 (p0) REVERT: A 546 LYS cc_start: 0.8429 (mmtm) cc_final: 0.8207 (mtpp) REVERT: A 564 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8081 (ttmm) REVERT: A 684 GLN cc_start: 0.8279 (tp40) cc_final: 0.8016 (tp40) REVERT: A 687 ASP cc_start: 0.7845 (t70) cc_final: 0.7527 (t0) REVERT: A 696 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6895 (mm-40) REVERT: A 730 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: B 21 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8193 (p) REVERT: B 79 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7357 (ttm170) REVERT: B 237 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8509 (mtpt) REVERT: B 245 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8124 (ttmt) REVERT: B 255 TYR cc_start: 0.8789 (m-10) cc_final: 0.8051 (m-10) REVERT: B 276 LEU cc_start: 0.8679 (tt) cc_final: 0.8442 (tt) REVERT: B 289 ASN cc_start: 0.8377 (t0) cc_final: 0.8057 (t0) REVERT: B 370 VAL cc_start: 0.8606 (t) cc_final: 0.8351 (t) REVERT: B 377 TYR cc_start: 0.8228 (p90) cc_final: 0.7919 (p90) REVERT: B 384 GLU cc_start: 0.8041 (tp30) cc_final: 0.7743 (tp30) REVERT: B 385 PHE cc_start: 0.8613 (m-80) cc_final: 0.8042 (m-80) REVERT: B 414 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 415 SER cc_start: 0.8389 (p) cc_final: 0.7911 (m) REVERT: B 459 LYS cc_start: 0.8149 (tppp) cc_final: 0.7817 (tppp) REVERT: B 475 ASN cc_start: 0.8341 (t0) cc_final: 0.8108 (t0) REVERT: B 492 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8478 (pt) REVERT: B 531 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8313 (mmmt) REVERT: B 538 ASN cc_start: 0.7828 (p0) cc_final: 0.7534 (p0) REVERT: B 560 ASP cc_start: 0.7988 (m-30) cc_final: 0.7716 (m-30) REVERT: B 652 LYS cc_start: 0.6399 (pttt) cc_final: 0.6018 (pttt) REVERT: B 681 LYS cc_start: 0.8399 (mptt) cc_final: 0.8168 (mptt) REVERT: B 682 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 687 ASP cc_start: 0.7932 (t70) cc_final: 0.7650 (t70) outliers start: 47 outliers final: 35 residues processed: 321 average time/residue: 0.1288 time to fit residues: 54.1012 Evaluate side-chains 343 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 31 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 75 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107209 restraints weight = 15411.881| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.07 r_work: 0.3268 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10400 Z= 0.171 Angle : 0.596 11.891 14136 Z= 0.314 Chirality : 0.043 0.173 1718 Planarity : 0.004 0.052 1758 Dihedral : 4.648 55.319 1421 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 4.10 % Allowed : 19.25 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1322 helix: 0.78 (0.18), residues: 880 sheet: -0.55 (0.95), residues: 36 loop : -2.00 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.024 0.002 TYR A 377 PHE 0.023 0.001 PHE A 130 TRP 0.009 0.001 TRP B 482 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00384 (10400) covalent geometry : angle 0.59566 (14136) hydrogen bonds : bond 0.04292 ( 573) hydrogen bonds : angle 3.76280 ( 1671) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 290 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8216 (p) REVERT: A 129 VAL cc_start: 0.7802 (m) cc_final: 0.7465 (p) REVERT: A 235 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7712 (mm-40) REVERT: A 245 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8237 (ttmt) REVERT: A 272 PHE cc_start: 0.8572 (t80) cc_final: 0.8311 (t80) REVERT: A 287 GLU cc_start: 0.7640 (pp20) cc_final: 0.7209 (pp20) REVERT: A 369 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8048 (mttp) REVERT: A 370 VAL cc_start: 0.8625 (t) cc_final: 0.8350 (t) REVERT: A 377 TYR cc_start: 0.8001 (p90) cc_final: 0.7787 (p90) REVERT: A 384 GLU cc_start: 0.7951 (tp30) cc_final: 0.7548 (tp30) REVERT: A 385 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: A 538 ASN cc_start: 0.7918 (p0) cc_final: 0.7605 (p0) REVERT: A 564 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8079 (ttmm) REVERT: A 684 GLN cc_start: 0.8266 (tp40) cc_final: 0.8014 (tp40) REVERT: A 687 ASP cc_start: 0.7848 (t70) cc_final: 0.7547 (t0) REVERT: A 730 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: B 21 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8186 (p) REVERT: B 77 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8355 (ttmm) REVERT: B 79 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7358 (ttm170) REVERT: B 245 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8081 (ttmt) REVERT: B 255 TYR cc_start: 0.8790 (m-10) cc_final: 0.8055 (m-10) REVERT: B 276 LEU cc_start: 0.8680 (tt) cc_final: 0.8444 (tt) REVERT: B 286 LYS cc_start: 0.8517 (tppp) cc_final: 0.8252 (ttmt) REVERT: B 289 ASN cc_start: 0.8377 (t0) cc_final: 0.8046 (t0) REVERT: B 370 VAL cc_start: 0.8602 (t) cc_final: 0.8341 (t) REVERT: B 377 TYR cc_start: 0.8235 (p90) cc_final: 0.7913 (p90) REVERT: B 384 GLU cc_start: 0.8019 (tp30) cc_final: 0.7731 (tp30) REVERT: B 385 PHE cc_start: 0.8604 (m-80) cc_final: 0.8122 (m-80) REVERT: B 414 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7121 (tm-30) REVERT: B 415 SER cc_start: 0.8382 (p) cc_final: 0.7943 (m) REVERT: B 475 ASN cc_start: 0.8292 (t0) cc_final: 0.8046 (t0) REVERT: B 492 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8489 (pt) REVERT: B 538 ASN cc_start: 0.7866 (p0) cc_final: 0.7575 (p0) REVERT: B 560 ASP cc_start: 0.7988 (m-30) cc_final: 0.7716 (m-30) REVERT: B 580 LYS cc_start: 0.7482 (ttpt) cc_final: 0.6850 (ttpt) REVERT: B 652 LYS cc_start: 0.6441 (pttt) cc_final: 0.6058 (pttt) REVERT: B 681 LYS cc_start: 0.8398 (mptt) cc_final: 0.8164 (mptt) REVERT: B 682 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 687 ASP cc_start: 0.7923 (t70) cc_final: 0.7647 (t70) outliers start: 46 outliers final: 38 residues processed: 312 average time/residue: 0.1227 time to fit residues: 50.6430 Evaluate side-chains 332 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 289 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 0.0270 chunk 89 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108236 restraints weight = 15285.961| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.06 r_work: 0.3283 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10400 Z= 0.147 Angle : 0.581 11.373 14136 Z= 0.306 Chirality : 0.043 0.171 1718 Planarity : 0.004 0.050 1758 Dihedral : 4.629 56.683 1421 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 3.83 % Allowed : 20.32 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.24), residues: 1322 helix: 0.87 (0.18), residues: 878 sheet: -0.51 (0.95), residues: 36 loop : -1.96 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.024 0.001 TYR A 377 PHE 0.024 0.001 PHE A 130 TRP 0.010 0.001 TRP B 482 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00329 (10400) covalent geometry : angle 0.58116 (14136) hydrogen bonds : bond 0.04103 ( 573) hydrogen bonds : angle 3.71900 ( 1671) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 129 VAL cc_start: 0.7747 (m) cc_final: 0.7417 (p) REVERT: A 245 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8163 (ttmt) REVERT: A 369 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8068 (mttp) REVERT: A 370 VAL cc_start: 0.8615 (t) cc_final: 0.8347 (t) REVERT: A 377 TYR cc_start: 0.7976 (p90) cc_final: 0.7710 (p90) REVERT: A 384 GLU cc_start: 0.7943 (tp30) cc_final: 0.7539 (tp30) REVERT: A 385 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: A 475 ASN cc_start: 0.8265 (t0) cc_final: 0.8035 (t0) REVERT: A 531 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8228 (mmtt) REVERT: A 538 ASN cc_start: 0.7877 (p0) cc_final: 0.7531 (p0) REVERT: A 564 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8074 (ttmm) REVERT: A 677 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7729 (ttp80) REVERT: A 681 LYS cc_start: 0.8215 (mptt) cc_final: 0.7952 (mptt) REVERT: A 684 GLN cc_start: 0.8259 (tp40) cc_final: 0.7998 (tp40) REVERT: A 687 ASP cc_start: 0.7859 (t70) cc_final: 0.7550 (t0) REVERT: A 730 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: B 21 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8172 (p) REVERT: B 77 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8352 (ttmm) REVERT: B 79 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7362 (ttm170) REVERT: B 245 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8068 (ttmt) REVERT: B 255 TYR cc_start: 0.8777 (m-10) cc_final: 0.8058 (m-10) REVERT: B 276 LEU cc_start: 0.8671 (tt) cc_final: 0.8424 (tt) REVERT: B 286 LYS cc_start: 0.8512 (tppp) cc_final: 0.8252 (ttmt) REVERT: B 289 ASN cc_start: 0.8360 (t0) cc_final: 0.8032 (t0) REVERT: B 370 VAL cc_start: 0.8578 (t) cc_final: 0.8321 (t) REVERT: B 377 TYR cc_start: 0.8190 (p90) cc_final: 0.7831 (p90) REVERT: B 384 GLU cc_start: 0.8025 (tp30) cc_final: 0.7728 (tp30) REVERT: B 385 PHE cc_start: 0.8579 (m-80) cc_final: 0.7973 (m-80) REVERT: B 414 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7109 (tm-30) REVERT: B 415 SER cc_start: 0.8359 (p) cc_final: 0.7931 (m) REVERT: B 475 ASN cc_start: 0.8337 (t0) cc_final: 0.8105 (t0) REVERT: B 492 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8476 (pt) REVERT: B 538 ASN cc_start: 0.7825 (p0) cc_final: 0.7534 (p0) REVERT: B 560 ASP cc_start: 0.7991 (m-30) cc_final: 0.7710 (m-30) REVERT: B 580 LYS cc_start: 0.7435 (ttpt) cc_final: 0.6815 (ttpt) REVERT: B 652 LYS cc_start: 0.6362 (pttt) cc_final: 0.6041 (pttt) REVERT: B 681 LYS cc_start: 0.8393 (mptt) cc_final: 0.8164 (mptt) REVERT: B 682 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7501 (mm-30) REVERT: B 687 ASP cc_start: 0.7945 (t70) cc_final: 0.7684 (t70) outliers start: 43 outliers final: 35 residues processed: 316 average time/residue: 0.1225 time to fit residues: 51.3771 Evaluate side-chains 328 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 0.0370 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107729 restraints weight = 15428.156| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.07 r_work: 0.3289 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10400 Z= 0.166 Angle : 0.600 11.480 14136 Z= 0.316 Chirality : 0.043 0.182 1718 Planarity : 0.004 0.051 1758 Dihedral : 4.640 56.569 1421 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 4.01 % Allowed : 20.59 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1322 helix: 0.86 (0.18), residues: 882 sheet: -0.58 (0.94), residues: 36 loop : -2.00 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.023 0.002 TYR A 377 PHE 0.024 0.001 PHE A 130 TRP 0.009 0.001 TRP B 482 HIS 0.002 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00375 (10400) covalent geometry : angle 0.60042 (14136) hydrogen bonds : bond 0.04224 ( 573) hydrogen bonds : angle 3.74703 ( 1671) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.62 seconds wall clock time: 46 minutes 44.96 seconds (2804.96 seconds total)