Starting phenix.real_space_refine on Sun Dec 29 08:33:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wl2_32574/12_2024/7wl2_32574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wl2_32574/12_2024/7wl2_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_32574/12_2024/7wl2_32574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wl2_32574/12_2024/7wl2_32574.map" model { file = "/net/cci-nas-00/data/ceres_data/7wl2_32574/12_2024/7wl2_32574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wl2_32574/12_2024/7wl2_32574.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.69, per 1000 atoms: 0.66 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: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.11 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: 3.13 Time building geometry restraints manager: 3.08 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: 0.00 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: 6.340 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 25.410 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- 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= 0.119 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.000 TRP A 83 HIS 0.002 0.000 HIS B 656 PHE 0.009 0.001 PHE B 555 TYR 0.007 0.001 TYR A 377 ARG 0.001 0.000 ARG B 512 *********************** 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 : 1.075 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: 0.5758 (tmtt) REVERT: A 652 LYS cc_start: 0.5141 (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: 0.8097 (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: 0.2800 time to fit residues: 145.7731 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 : 1.195 ------------------------------------------------------------------------------- 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 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 262 GLN 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2416 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= 0.286 Angle : 0.611 10.936 14136 Z= 0.319 Chirality : 0.044 0.210 1718 Planarity : 0.005 0.053 1758 Dihedral : 5.059 56.288 1432 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.39 % Allowed : 14.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.22), residues: 1322 helix: -0.50 (0.17), residues: 866 sheet: -3.21 (0.66), residues: 36 loop : -2.71 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.011 0.001 HIS A 656 PHE 0.026 0.002 PHE B 130 TYR 0.020 0.002 TYR B 377 ARG 0.006 0.001 ARG B 717 *********************** 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 364 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 326 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8304 (tpp-160) cc_final: 0.7797 (mmt-90) REVERT: A 79 ARG cc_start: 0.6883 (mtt-85) cc_final: 0.6647 (mmm160) REVERT: A 182 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.6263 (p0) REVERT: A 237 LYS cc_start: 0.8420 (ttpp) cc_final: 0.8135 (ttpt) REVERT: A 247 TYR cc_start: 0.7984 (m-10) cc_final: 0.6838 (m-80) REVERT: A 287 GLU cc_start: 0.7141 (pp20) cc_final: 0.6784 (pp20) REVERT: A 361 TYR cc_start: 0.8205 (t80) cc_final: 0.7687 (t80) REVERT: A 369 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7651 (mttm) REVERT: A 371 TYR cc_start: 0.8005 (m-80) cc_final: 0.7748 (m-80) REVERT: A 377 TYR cc_start: 0.7709 (p90) cc_final: 0.7435 (p90) REVERT: A 384 GLU cc_start: 0.7424 (tp30) cc_final: 0.6849 (tp30) REVERT: A 385 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.6968 (t80) REVERT: A 414 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6659 (tm-30) REVERT: A 415 SER cc_start: 0.8154 (p) cc_final: 0.7910 (m) REVERT: A 432 MET cc_start: 0.7650 (tpt) cc_final: 0.7041 (tpt) REVERT: A 448 SER cc_start: 0.8159 (p) cc_final: 0.7946 (p) REVERT: A 459 LYS cc_start: 0.7445 (tppp) cc_final: 0.7098 (tppp) REVERT: A 475 ASN cc_start: 0.7958 (t0) cc_final: 0.7403 (t0) REVERT: A 503 LEU cc_start: 0.8065 (mt) cc_final: 0.7849 (mm) REVERT: A 518 TRP cc_start: 0.8604 (p-90) cc_final: 0.8335 (p-90) REVERT: A 576 ARG cc_start: 0.7512 (mtt90) cc_final: 0.7226 (ttm-80) REVERT: A 580 LYS cc_start: 0.6569 (ttpt) cc_final: 0.6173 (ttpt) REVERT: A 652 LYS cc_start: 0.5224 (pttt) cc_final: 0.4100 (pttt) REVERT: A 669 ASP cc_start: 0.6546 (t0) cc_final: 0.6303 (t0) REVERT: A 677 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.7151 (ttp80) REVERT: A 681 LYS cc_start: 0.7567 (tptt) cc_final: 0.7345 (mptt) REVERT: A 684 GLN cc_start: 0.7985 (tp40) cc_final: 0.7698 (tp40) REVERT: A 687 ASP cc_start: 0.7313 (t70) cc_final: 0.6996 (t0) REVERT: A 696 GLN cc_start: 0.6648 (mm-40) cc_final: 0.6369 (mm-40) REVERT: B 137 SER cc_start: 0.8132 (p) cc_final: 0.7888 (t) REVERT: B 245 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7669 (ttmt) REVERT: B 255 TYR cc_start: 0.8384 (m-10) cc_final: 0.7621 (m-80) REVERT: B 289 ASN cc_start: 0.8126 (t0) cc_final: 0.7789 (t0) REVERT: B 309 ILE cc_start: 0.8456 (tt) cc_final: 0.8216 (pt) REVERT: B 320 GLU cc_start: 0.6756 (tp30) cc_final: 0.6535 (tp30) REVERT: B 361 TYR cc_start: 0.8211 (t80) cc_final: 0.7412 (t80) REVERT: B 370 VAL cc_start: 0.8441 (t) cc_final: 0.8213 (t) REVERT: B 384 GLU cc_start: 0.7639 (tp30) cc_final: 0.7369 (tp30) REVERT: B 385 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: B 462 PHE cc_start: 0.8134 (m-10) cc_final: 0.7834 (m-10) REVERT: B 475 ASN cc_start: 0.8014 (t0) cc_final: 0.7741 (t0) REVERT: B 492 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8163 (pt) REVERT: B 538 ASN cc_start: 0.6897 (p0) cc_final: 0.6580 (p0) REVERT: B 549 ARG cc_start: 0.8154 (ttt90) cc_final: 0.7572 (ttt90) REVERT: B 560 ASP cc_start: 0.7319 (m-30) cc_final: 0.7061 (m-30) REVERT: B 564 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7746 (ttmm) REVERT: B 580 LYS cc_start: 0.6851 (ttpt) cc_final: 0.6465 (tmtt) REVERT: B 661 ASP cc_start: 0.7663 (t0) cc_final: 0.7446 (t0) REVERT: B 669 ASP cc_start: 0.6688 (t0) cc_final: 0.6474 (t0) REVERT: B 681 LYS cc_start: 0.8103 (mptt) cc_final: 0.7789 (mptt) REVERT: B 682 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6662 (mm-30) REVERT: B 685 ARG cc_start: 0.8251 (mtm180) cc_final: 0.7444 (mtm180) REVERT: B 687 ASP cc_start: 0.7243 (t70) cc_final: 0.7040 (t0) REVERT: B 702 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7958 (ttmm) REVERT: B 731 ASN cc_start: 0.7188 (m110) cc_final: 0.6977 (m110) outliers start: 38 outliers final: 23 residues processed: 340 average time/residue: 0.3028 time to fit residues: 135.3195 Evaluate side-chains 328 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 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 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10400 Z= 0.267 Angle : 0.583 10.031 14136 Z= 0.307 Chirality : 0.043 0.152 1718 Planarity : 0.004 0.053 1758 Dihedral : 4.960 59.854 1426 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.55 % Allowed : 16.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1322 helix: 0.21 (0.18), residues: 856 sheet: -2.60 (0.73), residues: 36 loop : -2.16 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.003 0.001 HIS B 656 PHE 0.014 0.001 PHE B 130 TYR 0.021 0.002 TYR B 377 ARG 0.007 0.001 ARG B 677 *********************** 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 363 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 312 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8105 (p) REVERT: A 36 ARG cc_start: 0.8340 (tpp-160) cc_final: 0.7790 (mmt-90) REVERT: A 182 ASP cc_start: 0.6500 (OUTLIER) cc_final: 0.6198 (p0) REVERT: A 237 LYS cc_start: 0.8453 (ttpp) cc_final: 0.8218 (ttpt) REVERT: A 248 ASN cc_start: 0.7797 (m-40) cc_final: 0.7545 (m-40) REVERT: A 287 GLU cc_start: 0.7151 (pp20) cc_final: 0.6758 (pp20) REVERT: A 323 TYR cc_start: 0.7929 (m-10) cc_final: 0.7720 (m-10) REVERT: A 384 GLU cc_start: 0.7525 (tp30) cc_final: 0.7033 (tp30) REVERT: A 385 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.6997 (t80) REVERT: A 414 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6697 (tm-30) REVERT: A 415 SER cc_start: 0.8145 (p) cc_final: 0.7942 (m) REVERT: A 448 SER cc_start: 0.8140 (p) cc_final: 0.7860 (p) REVERT: A 459 LYS cc_start: 0.7514 (tppp) cc_final: 0.7175 (tppp) REVERT: A 475 ASN cc_start: 0.7937 (t0) cc_final: 0.7300 (t0) REVERT: A 538 ASN cc_start: 0.7004 (p0) cc_final: 0.6655 (p0) REVERT: A 564 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7781 (ttmm) REVERT: A 576 ARG cc_start: 0.7521 (mtt90) cc_final: 0.7244 (ttm-80) REVERT: A 580 LYS cc_start: 0.6560 (ttpt) cc_final: 0.6165 (ttpt) REVERT: A 677 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.7116 (ttp80) REVERT: A 681 LYS cc_start: 0.7635 (mptt) cc_final: 0.7379 (mptt) REVERT: A 684 GLN cc_start: 0.7996 (tp40) cc_final: 0.7698 (tp-100) REVERT: A 687 ASP cc_start: 0.7290 (t70) cc_final: 0.6953 (t0) REVERT: A 730 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: B 21 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8097 (p) REVERT: B 203 PHE cc_start: 0.8565 (m-10) cc_final: 0.8360 (m-10) REVERT: B 245 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7691 (ttmt) REVERT: B 255 TYR cc_start: 0.8392 (m-10) cc_final: 0.7560 (m-80) REVERT: B 276 LEU cc_start: 0.8477 (tt) cc_final: 0.8273 (tt) REVERT: B 289 ASN cc_start: 0.8136 (t0) cc_final: 0.7796 (t0) REVERT: B 303 GLU cc_start: 0.6918 (mp0) cc_final: 0.6692 (mp0) REVERT: B 320 GLU cc_start: 0.6875 (tp30) cc_final: 0.6654 (tp30) REVERT: B 361 TYR cc_start: 0.8192 (t80) cc_final: 0.7386 (t80) REVERT: B 370 VAL cc_start: 0.8435 (t) cc_final: 0.8195 (t) REVERT: B 384 GLU cc_start: 0.7605 (tp30) cc_final: 0.7312 (tp30) REVERT: B 385 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7644 (m-80) REVERT: B 414 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6750 (tm-30) REVERT: B 459 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7396 (tppp) REVERT: B 462 PHE cc_start: 0.8163 (m-10) cc_final: 0.7850 (m-10) REVERT: B 475 ASN cc_start: 0.7987 (t0) cc_final: 0.7697 (t0) REVERT: B 492 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8198 (pt) REVERT: B 528 ASP cc_start: 0.8481 (p0) cc_final: 0.8021 (p0) REVERT: B 538 ASN cc_start: 0.6976 (p0) cc_final: 0.6634 (p0) REVERT: B 560 ASP cc_start: 0.7316 (m-30) cc_final: 0.7005 (m-30) REVERT: B 576 ARG cc_start: 0.7365 (mtt90) cc_final: 0.7098 (mtt90) REVERT: B 587 ARG cc_start: 0.5985 (tpp-160) cc_final: 0.5567 (tpp-160) REVERT: B 669 ASP cc_start: 0.6676 (t0) cc_final: 0.6435 (t0) REVERT: B 681 LYS cc_start: 0.7980 (mptt) cc_final: 0.7694 (mptt) REVERT: B 687 ASP cc_start: 0.7235 (t70) cc_final: 0.6917 (t70) outliers start: 51 outliers final: 33 residues processed: 336 average time/residue: 0.2902 time to fit residues: 127.9964 Evaluate side-chains 340 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 299 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 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 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 279 ILE Chi-restraints excluded: chain B residue 298 VAL 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 459 LYS 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 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0040 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 HIS B 684 GLN B 696 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10400 Z= 0.211 Angle : 0.560 8.283 14136 Z= 0.295 Chirality : 0.042 0.158 1718 Planarity : 0.004 0.050 1758 Dihedral : 4.961 58.748 1426 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 4.63 % Allowed : 16.40 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1322 helix: 0.59 (0.18), residues: 856 sheet: -2.00 (0.81), residues: 36 loop : -2.02 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS B 160 PHE 0.012 0.001 PHE A 115 TYR 0.017 0.001 TYR B 377 ARG 0.006 0.001 ARG B 38 *********************** 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 358 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 306 time to evaluate : 1.154 Fit side-chains REVERT: A 21 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8143 (p) REVERT: A 182 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6299 (p0) REVERT: A 248 ASN cc_start: 0.7812 (m-40) cc_final: 0.7564 (m-40) REVERT: A 287 GLU cc_start: 0.7138 (pp20) cc_final: 0.6745 (pp20) REVERT: A 370 VAL cc_start: 0.8361 (t) cc_final: 0.8134 (t) REVERT: A 384 GLU cc_start: 0.7498 (tp30) cc_final: 0.7036 (tp30) REVERT: A 385 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7069 (t80) REVERT: A 414 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6655 (tm-30) REVERT: A 415 SER cc_start: 0.8122 (p) cc_final: 0.7910 (m) REVERT: A 459 LYS cc_start: 0.7541 (tppp) cc_final: 0.7296 (tppp) REVERT: A 475 ASN cc_start: 0.7902 (t0) cc_final: 0.7087 (t0) REVERT: A 478 ASP cc_start: 0.7304 (m-30) cc_final: 0.6023 (m-30) REVERT: A 538 ASN cc_start: 0.7027 (p0) cc_final: 0.6506 (p0) REVERT: A 546 LYS cc_start: 0.8140 (mmtm) cc_final: 0.7898 (mmmm) REVERT: A 564 LYS cc_start: 0.8008 (ttmm) cc_final: 0.7708 (ttmm) REVERT: A 576 ARG cc_start: 0.7506 (mtt90) cc_final: 0.7233 (ttm-80) REVERT: A 580 LYS cc_start: 0.6591 (ttpt) cc_final: 0.6170 (ttpt) REVERT: A 677 ARG cc_start: 0.7286 (ttm-80) cc_final: 0.7039 (ttp80) REVERT: A 681 LYS cc_start: 0.7612 (mptt) cc_final: 0.7372 (mptt) REVERT: A 684 GLN cc_start: 0.7988 (tp40) cc_final: 0.7715 (tp40) REVERT: A 687 ASP cc_start: 0.7288 (t70) cc_final: 0.6920 (t0) REVERT: A 730 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: B 21 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8108 (p) REVERT: B 134 ARG cc_start: 0.7258 (mtt90) cc_final: 0.7039 (mtt-85) REVERT: B 138 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8416 (m) REVERT: B 203 PHE cc_start: 0.8511 (m-10) cc_final: 0.8263 (m-10) REVERT: B 245 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7731 (ttmt) REVERT: B 255 TYR cc_start: 0.8399 (m-10) cc_final: 0.7589 (m-10) REVERT: B 276 LEU cc_start: 0.8453 (tt) cc_final: 0.8236 (tt) REVERT: B 289 ASN cc_start: 0.8088 (t0) cc_final: 0.7748 (t0) REVERT: B 320 GLU cc_start: 0.6877 (tp30) cc_final: 0.6657 (tp30) REVERT: B 361 TYR cc_start: 0.8151 (t80) cc_final: 0.7350 (t80) REVERT: B 370 VAL cc_start: 0.8416 (t) cc_final: 0.8191 (t) REVERT: B 384 GLU cc_start: 0.7595 (tp30) cc_final: 0.7280 (tp30) REVERT: B 385 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: B 414 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6716 (tm-30) REVERT: B 459 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7394 (tppp) REVERT: B 462 PHE cc_start: 0.8164 (m-10) cc_final: 0.7817 (m-10) REVERT: B 475 ASN cc_start: 0.7968 (t0) cc_final: 0.7680 (t0) REVERT: B 492 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8227 (pt) REVERT: B 531 LYS cc_start: 0.8227 (mmtp) cc_final: 0.8003 (mmtt) REVERT: B 538 ASN cc_start: 0.6971 (p0) cc_final: 0.6612 (p0) REVERT: B 560 ASP cc_start: 0.7312 (m-30) cc_final: 0.7000 (m-30) REVERT: B 587 ARG cc_start: 0.5802 (tpp-160) cc_final: 0.5462 (tpm170) REVERT: B 681 LYS cc_start: 0.7932 (mptt) cc_final: 0.7650 (mptt) REVERT: B 687 ASP cc_start: 0.7235 (t70) cc_final: 0.6879 (t70) REVERT: B 702 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7909 (ttmm) outliers start: 52 outliers final: 38 residues processed: 330 average time/residue: 0.2897 time to fit residues: 124.9147 Evaluate side-chains 328 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR 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 288 LEU 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 473 LYS 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 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 138 VAL 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 279 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 473 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 Chi-restraints excluded: chain B residue 716 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 0.0270 chunk 52 optimal weight: 0.5980 chunk 108 optimal weight: 0.3980 chunk 88 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 overall best weight: 0.1554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10400 Z= 0.147 Angle : 0.535 6.989 14136 Z= 0.282 Chirality : 0.041 0.157 1718 Planarity : 0.004 0.041 1758 Dihedral : 4.857 57.704 1426 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.81 % Allowed : 16.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1322 helix: 0.85 (0.18), residues: 860 sheet: -1.24 (0.92), residues: 36 loop : -1.84 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS B 375 PHE 0.011 0.001 PHE A 115 TYR 0.016 0.001 TYR B 377 ARG 0.006 0.000 ARG A 38 *********************** 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 339 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 97 VAL cc_start: 0.8207 (t) cc_final: 0.7938 (t) REVERT: A 134 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.6740 (mtt90) REVERT: A 182 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.6221 (p0) REVERT: A 248 ASN cc_start: 0.7699 (m-40) cc_final: 0.7463 (m-40) REVERT: A 286 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7937 (ttmm) REVERT: A 287 GLU cc_start: 0.7094 (pp20) cc_final: 0.6683 (pp20) REVERT: A 329 LYS cc_start: 0.7964 (pttt) cc_final: 0.7699 (ptmm) REVERT: A 384 GLU cc_start: 0.7485 (tp30) cc_final: 0.7061 (tp30) REVERT: A 414 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6637 (tm-30) REVERT: A 475 ASN cc_start: 0.7918 (t0) cc_final: 0.7578 (t0) REVERT: A 478 ASP cc_start: 0.7255 (m-30) cc_final: 0.6797 (m-30) REVERT: A 538 ASN cc_start: 0.6993 (p0) cc_final: 0.6647 (p0) REVERT: A 564 LYS cc_start: 0.7987 (ttmm) cc_final: 0.7700 (ttmm) REVERT: A 576 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7184 (ttm-80) REVERT: A 677 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6990 (ttp80) REVERT: A 681 LYS cc_start: 0.7580 (mptt) cc_final: 0.7326 (mptt) REVERT: A 684 GLN cc_start: 0.7996 (tp40) cc_final: 0.7715 (tp40) REVERT: A 687 ASP cc_start: 0.7268 (t70) cc_final: 0.6892 (t0) REVERT: A 730 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: B 21 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.8057 (p) REVERT: B 77 LYS cc_start: 0.8261 (ttmm) cc_final: 0.7941 (ttmm) REVERT: B 79 ARG cc_start: 0.7216 (ttm170) cc_final: 0.6790 (ttm170) REVERT: B 97 VAL cc_start: 0.8179 (t) cc_final: 0.7953 (t) REVERT: B 138 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8431 (p) REVERT: B 203 PHE cc_start: 0.8489 (m-10) cc_final: 0.8235 (m-10) REVERT: B 245 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7787 (ttmt) REVERT: B 255 TYR cc_start: 0.8375 (m-10) cc_final: 0.7598 (m-10) REVERT: B 276 LEU cc_start: 0.8350 (tt) cc_final: 0.8110 (tt) REVERT: B 277 LEU cc_start: 0.8529 (mt) cc_final: 0.8284 (mt) REVERT: B 289 ASN cc_start: 0.7996 (t0) cc_final: 0.7644 (t0) REVERT: B 323 TYR cc_start: 0.8029 (m-10) cc_final: 0.7826 (m-10) REVERT: B 361 TYR cc_start: 0.8135 (t80) cc_final: 0.7244 (t80) REVERT: B 370 VAL cc_start: 0.8405 (t) cc_final: 0.8176 (t) REVERT: B 378 VAL cc_start: 0.8200 (t) cc_final: 0.7821 (p) REVERT: B 384 GLU cc_start: 0.7513 (tp30) cc_final: 0.7218 (tp30) REVERT: B 385 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: B 414 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6549 (tm-30) REVERT: B 462 PHE cc_start: 0.8122 (m-10) cc_final: 0.7760 (m-80) REVERT: B 475 ASN cc_start: 0.7959 (t0) cc_final: 0.7679 (t0) REVERT: B 492 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8229 (pt) REVERT: B 538 ASN cc_start: 0.6914 (p0) cc_final: 0.6570 (p0) REVERT: B 560 ASP cc_start: 0.7314 (m-30) cc_final: 0.6991 (m-30) REVERT: B 576 ARG cc_start: 0.7279 (mtt90) cc_final: 0.7036 (mtt180) REVERT: B 580 LYS cc_start: 0.6844 (ttpt) cc_final: 0.6344 (tmtt) REVERT: B 652 LYS cc_start: 0.5620 (pttt) cc_final: 0.4609 (pttt) REVERT: B 681 LYS cc_start: 0.7899 (mptt) cc_final: 0.7622 (mptt) REVERT: B 685 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7615 (mtm180) REVERT: B 687 ASP cc_start: 0.7193 (t70) cc_final: 0.6891 (t70) REVERT: B 696 GLN cc_start: 0.6603 (mm-40) cc_final: 0.6310 (mm-40) outliers start: 54 outliers final: 33 residues processed: 313 average time/residue: 0.2611 time to fit residues: 109.3847 Evaluate side-chains 316 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 473 LYS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 582 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 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 138 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE 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 473 LYS 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 114 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10400 Z= 0.255 Angle : 0.580 7.263 14136 Z= 0.306 Chirality : 0.043 0.162 1718 Planarity : 0.004 0.048 1758 Dihedral : 4.989 59.755 1426 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % Rotamer: Outliers : 4.72 % Allowed : 16.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1322 helix: 0.81 (0.18), residues: 872 sheet: -1.08 (0.91), residues: 36 loop : -1.94 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 160 PHE 0.018 0.001 PHE A 130 TYR 0.014 0.002 TYR A 361 ARG 0.009 0.001 ARG B 134 *********************** 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 332 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 1.258 Fit side-chains REVERT: A 21 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8180 (p) REVERT: A 182 ASP cc_start: 0.6554 (OUTLIER) cc_final: 0.6347 (p0) REVERT: A 247 TYR cc_start: 0.7950 (m-10) cc_final: 0.6972 (m-80) REVERT: A 248 ASN cc_start: 0.7779 (m-40) cc_final: 0.7552 (m-40) REVERT: A 259 GLU cc_start: 0.7308 (tt0) cc_final: 0.6617 (tt0) REVERT: A 286 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7950 (ttmm) REVERT: A 287 GLU cc_start: 0.7133 (pp20) cc_final: 0.6719 (pp20) REVERT: A 329 LYS cc_start: 0.8084 (pttt) cc_final: 0.7787 (ptmm) REVERT: A 378 VAL cc_start: 0.8199 (t) cc_final: 0.7823 (p) REVERT: A 384 GLU cc_start: 0.7540 (tp30) cc_final: 0.7091 (tp30) REVERT: A 414 GLU cc_start: 0.6889 (tm-30) cc_final: 0.6644 (tm-30) REVERT: A 475 ASN cc_start: 0.7913 (t0) cc_final: 0.7456 (t0) REVERT: A 478 ASP cc_start: 0.7266 (m-30) cc_final: 0.6755 (m-30) REVERT: A 538 ASN cc_start: 0.7134 (p0) cc_final: 0.6630 (p0) REVERT: A 564 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7711 (ttmm) REVERT: A 580 LYS cc_start: 0.6609 (ttpt) cc_final: 0.5927 (tmtt) REVERT: A 681 LYS cc_start: 0.7607 (mptt) cc_final: 0.7294 (mmtp) REVERT: A 684 GLN cc_start: 0.7997 (tp40) cc_final: 0.7733 (tp40) REVERT: A 687 ASP cc_start: 0.7277 (t70) cc_final: 0.6922 (t0) REVERT: A 730 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: B 21 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 77 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7936 (ttmm) REVERT: B 79 ARG cc_start: 0.7282 (ttm170) cc_final: 0.6918 (ttm170) REVERT: B 138 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8451 (p) REVERT: B 203 PHE cc_start: 0.8447 (m-10) cc_final: 0.8181 (m-10) REVERT: B 245 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7771 (ttmt) REVERT: B 255 TYR cc_start: 0.8389 (m-10) cc_final: 0.7581 (m-10) REVERT: B 276 LEU cc_start: 0.8360 (tt) cc_final: 0.8142 (tt) REVERT: B 277 LEU cc_start: 0.8536 (mt) cc_final: 0.8289 (mt) REVERT: B 323 TYR cc_start: 0.8068 (m-10) cc_final: 0.7854 (m-10) REVERT: B 361 TYR cc_start: 0.8159 (t80) cc_final: 0.7286 (t80) REVERT: B 370 VAL cc_start: 0.8420 (t) cc_final: 0.8181 (t) REVERT: B 384 GLU cc_start: 0.7580 (tp30) cc_final: 0.7267 (tp30) REVERT: B 385 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: B 414 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6642 (tm-30) REVERT: B 462 PHE cc_start: 0.8131 (m-10) cc_final: 0.7756 (m-80) REVERT: B 475 ASN cc_start: 0.7895 (t0) cc_final: 0.7629 (t0) REVERT: B 492 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8275 (pt) REVERT: B 538 ASN cc_start: 0.7002 (p0) cc_final: 0.6630 (p0) REVERT: B 560 ASP cc_start: 0.7315 (m-30) cc_final: 0.7003 (m-30) REVERT: B 580 LYS cc_start: 0.6839 (ttpt) cc_final: 0.6308 (ttpt) REVERT: B 681 LYS cc_start: 0.7884 (mptt) cc_final: 0.7615 (mptt) REVERT: B 685 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7668 (mtm180) REVERT: B 687 ASP cc_start: 0.7166 (t70) cc_final: 0.6872 (t70) outliers start: 53 outliers final: 37 residues processed: 306 average time/residue: 0.2681 time to fit residues: 109.6476 Evaluate side-chains 320 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 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 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 473 LYS 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 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 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 194 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 321 LYS Chi-restraints excluded: chain B residue 339 VAL 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 668 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 716 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 0.0270 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 0.0980 chunk 127 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN B 696 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10400 Z= 0.191 Angle : 0.571 11.795 14136 Z= 0.298 Chirality : 0.042 0.164 1718 Planarity : 0.004 0.045 1758 Dihedral : 4.735 48.204 1424 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 4.55 % Allowed : 17.47 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1322 helix: 0.88 (0.18), residues: 876 sheet: -0.81 (0.92), residues: 36 loop : -1.89 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.000 HIS B 723 PHE 0.024 0.001 PHE A 385 TYR 0.026 0.001 TYR A 361 ARG 0.010 0.001 ARG B 134 *********************** 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 330 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 66 LYS cc_start: 0.8120 (tptp) cc_final: 0.7642 (tptp) REVERT: A 247 TYR cc_start: 0.7927 (m-10) cc_final: 0.6875 (m-80) REVERT: A 248 ASN cc_start: 0.7749 (m-40) cc_final: 0.7524 (m-40) REVERT: A 286 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7924 (ttmm) REVERT: A 287 GLU cc_start: 0.7131 (pp20) cc_final: 0.6726 (pp20) REVERT: A 329 LYS cc_start: 0.8007 (pttt) cc_final: 0.7725 (ptmm) REVERT: A 378 VAL cc_start: 0.8189 (t) cc_final: 0.7815 (p) REVERT: A 384 GLU cc_start: 0.7539 (tp30) cc_final: 0.7171 (tp30) REVERT: A 385 PHE cc_start: 0.8524 (m-80) cc_final: 0.8114 (m-80) REVERT: A 414 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6679 (tm-30) REVERT: A 432 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7308 (tmm) REVERT: A 475 ASN cc_start: 0.7890 (t0) cc_final: 0.7439 (t0) REVERT: A 478 ASP cc_start: 0.7311 (m-30) cc_final: 0.6782 (m-30) REVERT: A 538 ASN cc_start: 0.7129 (p0) cc_final: 0.6635 (p0) REVERT: A 564 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7683 (ttmm) REVERT: A 681 LYS cc_start: 0.7587 (mptt) cc_final: 0.7347 (mptt) REVERT: A 684 GLN cc_start: 0.7993 (tp40) cc_final: 0.7727 (tp40) REVERT: A 687 ASP cc_start: 0.7274 (t70) cc_final: 0.6916 (t0) REVERT: A 730 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: B 21 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8128 (p) REVERT: B 77 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7931 (ttmm) REVERT: B 79 ARG cc_start: 0.7258 (ttm170) cc_final: 0.6882 (ttm170) REVERT: B 138 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8435 (p) REVERT: B 178 THR cc_start: 0.7374 (OUTLIER) cc_final: 0.6972 (p) REVERT: B 203 PHE cc_start: 0.8434 (m-10) cc_final: 0.8155 (m-10) REVERT: B 245 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7771 (ttmt) REVERT: B 255 TYR cc_start: 0.8377 (m-10) cc_final: 0.7610 (m-10) REVERT: B 276 LEU cc_start: 0.8344 (tt) cc_final: 0.8134 (tt) REVERT: B 277 LEU cc_start: 0.8527 (mt) cc_final: 0.8288 (mt) REVERT: B 287 GLU cc_start: 0.7244 (pp20) cc_final: 0.6965 (pp20) REVERT: B 289 ASN cc_start: 0.8025 (t0) cc_final: 0.7677 (t0) REVERT: B 361 TYR cc_start: 0.8125 (t80) cc_final: 0.7228 (t80) REVERT: B 370 VAL cc_start: 0.8414 (t) cc_final: 0.8182 (t) REVERT: B 384 GLU cc_start: 0.7576 (tp30) cc_final: 0.7253 (tp30) REVERT: B 385 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: B 414 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6639 (tm-30) REVERT: B 475 ASN cc_start: 0.7950 (t0) cc_final: 0.7694 (t0) REVERT: B 492 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8264 (pt) REVERT: B 538 ASN cc_start: 0.6978 (p0) cc_final: 0.6605 (p0) REVERT: B 560 ASP cc_start: 0.7323 (m-30) cc_final: 0.7012 (m-30) REVERT: B 580 LYS cc_start: 0.6828 (ttpt) cc_final: 0.6305 (ttpt) REVERT: B 681 LYS cc_start: 0.7884 (mptt) cc_final: 0.7604 (mptt) REVERT: B 685 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7673 (mtm180) REVERT: B 687 ASP cc_start: 0.7165 (t70) cc_final: 0.6876 (t70) outliers start: 51 outliers final: 37 residues processed: 305 average time/residue: 0.2636 time to fit residues: 107.6058 Evaluate side-chains 322 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 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 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 473 LYS 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 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 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE 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 529 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 716 ASP 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 75 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 80 optimal weight: 0.0570 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 0.3980 chunk 111 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 ASN B 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10400 Z= 0.208 Angle : 0.581 11.377 14136 Z= 0.303 Chirality : 0.042 0.173 1718 Planarity : 0.004 0.046 1758 Dihedral : 4.455 48.399 1422 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 4.72 % Allowed : 17.56 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1322 helix: 0.94 (0.18), residues: 874 sheet: -0.64 (0.93), residues: 36 loop : -1.82 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.000 HIS B 723 PHE 0.019 0.001 PHE A 385 TYR 0.019 0.001 TYR A 361 ARG 0.010 0.001 ARG B 134 *********************** 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 330 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8177 (p) REVERT: A 66 LYS cc_start: 0.8098 (tptp) cc_final: 0.7634 (tptp) REVERT: A 247 TYR cc_start: 0.7899 (m-80) cc_final: 0.6849 (m-80) REVERT: A 248 ASN cc_start: 0.7742 (m-40) cc_final: 0.7511 (m-40) REVERT: A 286 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7926 (ttmm) REVERT: A 287 GLU cc_start: 0.7125 (pp20) cc_final: 0.6723 (pp20) REVERT: A 329 LYS cc_start: 0.7971 (pttt) cc_final: 0.7666 (ptmm) REVERT: A 378 VAL cc_start: 0.8197 (t) cc_final: 0.7807 (p) REVERT: A 384 GLU cc_start: 0.7550 (tp30) cc_final: 0.7185 (tp30) REVERT: A 414 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6680 (tm-30) REVERT: A 432 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7316 (tmm) REVERT: A 475 ASN cc_start: 0.7887 (t0) cc_final: 0.7423 (t0) REVERT: A 478 ASP cc_start: 0.7315 (m-30) cc_final: 0.6762 (m-30) REVERT: A 538 ASN cc_start: 0.7201 (p0) cc_final: 0.6715 (p0) REVERT: A 564 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7689 (ttmm) REVERT: A 681 LYS cc_start: 0.7608 (mptt) cc_final: 0.7358 (mptt) REVERT: A 684 GLN cc_start: 0.7983 (tp40) cc_final: 0.7645 (tp40) REVERT: A 687 ASP cc_start: 0.7279 (t70) cc_final: 0.6915 (t0) REVERT: A 730 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: B 21 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8124 (p) REVERT: B 77 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7928 (ttmm) REVERT: B 79 ARG cc_start: 0.7253 (ttm170) cc_final: 0.6864 (ttm170) REVERT: B 138 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 178 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7080 (p) REVERT: B 203 PHE cc_start: 0.8401 (m-10) cc_final: 0.8129 (m-10) REVERT: B 245 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7762 (ttmt) REVERT: B 255 TYR cc_start: 0.8380 (m-10) cc_final: 0.7617 (m-10) REVERT: B 272 PHE cc_start: 0.8396 (t80) cc_final: 0.8120 (t80) REVERT: B 276 LEU cc_start: 0.8348 (tt) cc_final: 0.8121 (tt) REVERT: B 277 LEU cc_start: 0.8513 (mt) cc_final: 0.8284 (mt) REVERT: B 287 GLU cc_start: 0.7232 (pp20) cc_final: 0.6998 (pp20) REVERT: B 289 ASN cc_start: 0.8051 (t0) cc_final: 0.7690 (t0) REVERT: B 361 TYR cc_start: 0.8128 (t80) cc_final: 0.7233 (t80) REVERT: B 370 VAL cc_start: 0.8414 (t) cc_final: 0.8179 (t) REVERT: B 384 GLU cc_start: 0.7577 (tp30) cc_final: 0.7258 (tp30) REVERT: B 385 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: B 414 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6601 (tm-30) REVERT: B 475 ASN cc_start: 0.7960 (t0) cc_final: 0.7664 (t0) REVERT: B 492 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8268 (pt) REVERT: B 538 ASN cc_start: 0.7004 (p0) cc_final: 0.6632 (p0) REVERT: B 560 ASP cc_start: 0.7297 (m-30) cc_final: 0.6986 (m-30) REVERT: B 580 LYS cc_start: 0.6835 (ttpt) cc_final: 0.6293 (ttpt) REVERT: B 681 LYS cc_start: 0.7870 (mptt) cc_final: 0.7617 (mptt) REVERT: B 685 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7640 (mtm180) REVERT: B 687 ASP cc_start: 0.7162 (t70) cc_final: 0.6876 (t70) outliers start: 53 outliers final: 39 residues processed: 302 average time/residue: 0.2626 time to fit residues: 105.8924 Evaluate side-chains 321 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 473 LYS 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 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE 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 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 678 MET Chi-restraints excluded: chain B residue 716 ASP 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 118 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3621 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= 0.231 Angle : 0.592 11.298 14136 Z= 0.311 Chirality : 0.043 0.190 1718 Planarity : 0.004 0.046 1758 Dihedral : 4.523 48.287 1422 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 4.37 % Allowed : 18.36 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1322 helix: 0.94 (0.18), residues: 874 sheet: -0.54 (0.94), residues: 36 loop : -1.80 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS A 160 PHE 0.019 0.001 PHE A 385 TYR 0.021 0.001 TYR A 361 ARG 0.010 0.001 ARG B 134 *********************** 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 325 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 1.273 Fit side-chains REVERT: A 21 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8179 (p) REVERT: A 66 LYS cc_start: 0.8092 (tptp) cc_final: 0.7620 (tptp) REVERT: A 247 TYR cc_start: 0.7847 (m-80) cc_final: 0.6921 (m-80) REVERT: A 248 ASN cc_start: 0.7748 (m-40) cc_final: 0.7511 (m-40) REVERT: A 286 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7925 (ttmm) REVERT: A 287 GLU cc_start: 0.7138 (pp20) cc_final: 0.6753 (pp20) REVERT: A 329 LYS cc_start: 0.7959 (pttt) cc_final: 0.7655 (ptmm) REVERT: A 384 GLU cc_start: 0.7533 (tp30) cc_final: 0.7184 (tp30) REVERT: A 414 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6685 (tm-30) REVERT: A 475 ASN cc_start: 0.7906 (t0) cc_final: 0.7437 (t0) REVERT: A 478 ASP cc_start: 0.7304 (m-30) cc_final: 0.6766 (m-30) REVERT: A 538 ASN cc_start: 0.7245 (p0) cc_final: 0.6780 (p0) REVERT: A 681 LYS cc_start: 0.7610 (mptt) cc_final: 0.7357 (mptt) REVERT: A 684 GLN cc_start: 0.7984 (tp40) cc_final: 0.7648 (tp40) REVERT: A 687 ASP cc_start: 0.7304 (t70) cc_final: 0.6967 (t0) REVERT: A 730 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: B 21 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8139 (p) REVERT: B 77 LYS cc_start: 0.8310 (ttmm) cc_final: 0.7935 (ttmm) REVERT: B 79 ARG cc_start: 0.7266 (ttm170) cc_final: 0.6878 (ttm170) REVERT: B 138 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8429 (p) REVERT: B 178 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7153 (p) REVERT: B 203 PHE cc_start: 0.8391 (m-10) cc_final: 0.8117 (m-10) REVERT: B 245 LYS cc_start: 0.8019 (ttmt) cc_final: 0.7753 (ttmt) REVERT: B 255 TYR cc_start: 0.8391 (m-10) cc_final: 0.7611 (m-10) REVERT: B 272 PHE cc_start: 0.8400 (t80) cc_final: 0.8162 (t80) REVERT: B 276 LEU cc_start: 0.8355 (tt) cc_final: 0.8117 (tt) REVERT: B 277 LEU cc_start: 0.8516 (mt) cc_final: 0.8287 (mt) REVERT: B 287 GLU cc_start: 0.7269 (pp20) cc_final: 0.7002 (pp20) REVERT: B 361 TYR cc_start: 0.8128 (t80) cc_final: 0.7238 (t80) REVERT: B 370 VAL cc_start: 0.8411 (t) cc_final: 0.8170 (t) REVERT: B 377 TYR cc_start: 0.7969 (p90) cc_final: 0.7574 (p90) REVERT: B 384 GLU cc_start: 0.7606 (tp30) cc_final: 0.7285 (tp30) REVERT: B 385 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: B 414 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6617 (tm-30) REVERT: B 475 ASN cc_start: 0.7944 (t0) cc_final: 0.7676 (t0) REVERT: B 492 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8283 (pt) REVERT: B 538 ASN cc_start: 0.7040 (p0) cc_final: 0.6661 (p0) REVERT: B 560 ASP cc_start: 0.7289 (m-30) cc_final: 0.6976 (m-30) REVERT: B 580 LYS cc_start: 0.6957 (ttpt) cc_final: 0.6396 (ttpt) REVERT: B 652 LYS cc_start: 0.5824 (pttt) cc_final: 0.4847 (pttt) REVERT: B 681 LYS cc_start: 0.7868 (mptt) cc_final: 0.7607 (mptt) REVERT: B 685 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7613 (mtm180) REVERT: B 687 ASP cc_start: 0.7153 (t70) cc_final: 0.6895 (t70) outliers start: 49 outliers final: 37 residues processed: 300 average time/residue: 0.2756 time to fit residues: 110.4482 Evaluate side-chains 319 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 274 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 433 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 473 LYS 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 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 80 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE 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 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 716 ASP 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 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 80 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10400 Z= 0.182 Angle : 0.581 10.735 14136 Z= 0.304 Chirality : 0.042 0.191 1718 Planarity : 0.004 0.043 1758 Dihedral : 4.453 49.623 1421 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1322 helix: 0.99 (0.18), residues: 872 sheet: -0.42 (0.95), residues: 36 loop : -1.96 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS A 160 PHE 0.019 0.001 PHE A 385 TYR 0.020 0.001 TYR A 361 ARG 0.010 0.001 ARG B 134 ********************** 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 322 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 275 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 21 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8152 (p) REVERT: A 66 LYS cc_start: 0.8075 (tptp) cc_final: 0.7618 (tptp) REVERT: A 134 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6702 (mtt90) REVERT: A 247 TYR cc_start: 0.7832 (m-80) cc_final: 0.6978 (m-80) REVERT: A 248 ASN cc_start: 0.7715 (m-40) cc_final: 0.7484 (m-40) REVERT: A 286 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7913 (ttmm) REVERT: A 329 LYS cc_start: 0.7891 (pttt) cc_final: 0.7597 (ptmm) REVERT: A 384 GLU cc_start: 0.7537 (tp30) cc_final: 0.7204 (tp30) REVERT: A 414 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 432 MET cc_start: 0.7932 (tmm) cc_final: 0.7138 (tmm) REVERT: A 475 ASN cc_start: 0.7918 (t0) cc_final: 0.7564 (t0) REVERT: A 478 ASP cc_start: 0.7311 (m-30) cc_final: 0.6750 (m-30) REVERT: A 538 ASN cc_start: 0.7211 (p0) cc_final: 0.6731 (p0) REVERT: A 681 LYS cc_start: 0.7616 (mptt) cc_final: 0.7362 (mptt) REVERT: A 684 GLN cc_start: 0.7990 (tp40) cc_final: 0.7650 (tp40) REVERT: A 687 ASP cc_start: 0.7301 (t70) cc_final: 0.6967 (t0) REVERT: A 730 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: B 21 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8096 (p) REVERT: B 77 LYS cc_start: 0.8301 (ttmm) cc_final: 0.7922 (ttmm) REVERT: B 79 ARG cc_start: 0.7244 (ttm170) cc_final: 0.6877 (ttm170) REVERT: B 178 THR cc_start: 0.7479 (OUTLIER) cc_final: 0.7124 (p) REVERT: B 203 PHE cc_start: 0.8368 (m-10) cc_final: 0.8092 (m-10) REVERT: B 245 LYS cc_start: 0.8027 (ttmt) cc_final: 0.7736 (ttmt) REVERT: B 255 TYR cc_start: 0.8370 (m-10) cc_final: 0.7603 (m-10) REVERT: B 272 PHE cc_start: 0.8375 (t80) cc_final: 0.8098 (t80) REVERT: B 276 LEU cc_start: 0.8337 (tt) cc_final: 0.8098 (tt) REVERT: B 277 LEU cc_start: 0.8518 (mt) cc_final: 0.8285 (mt) REVERT: B 361 TYR cc_start: 0.8101 (t80) cc_final: 0.7172 (t80) REVERT: B 370 VAL cc_start: 0.8398 (t) cc_final: 0.8159 (t) REVERT: B 377 TYR cc_start: 0.7911 (p90) cc_final: 0.7609 (p90) REVERT: B 384 GLU cc_start: 0.7575 (tp30) cc_final: 0.7275 (tp30) REVERT: B 385 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: B 414 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6576 (tm-30) REVERT: B 475 ASN cc_start: 0.7969 (t0) cc_final: 0.7705 (t0) REVERT: B 492 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8116 (pt) REVERT: B 538 ASN cc_start: 0.6987 (p0) cc_final: 0.6620 (p0) REVERT: B 560 ASP cc_start: 0.7300 (m-30) cc_final: 0.6986 (m-30) REVERT: B 580 LYS cc_start: 0.6882 (ttpt) cc_final: 0.6324 (ttpt) REVERT: B 652 LYS cc_start: 0.5835 (pttt) cc_final: 0.4747 (pttt) REVERT: B 681 LYS cc_start: 0.7857 (mptt) cc_final: 0.7607 (mptt) REVERT: B 682 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6024 (mm-30) REVERT: B 685 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7616 (mtm180) REVERT: B 687 ASP cc_start: 0.7153 (t70) cc_final: 0.6889 (t70) outliers start: 47 outliers final: 33 residues processed: 300 average time/residue: 0.2739 time to fit residues: 109.5756 Evaluate side-chains 312 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 279 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 473 LYS 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 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 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 178 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 385 PHE 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 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 716 ASP 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 96 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 107 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.122752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107101 restraints weight = 15479.544| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.06 r_work: 0.3284 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10400 Z= 0.276 Angle : 0.614 11.377 14136 Z= 0.324 Chirality : 0.044 0.196 1718 Planarity : 0.005 0.049 1758 Dihedral : 4.557 48.655 1421 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.35 % Favored : 93.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1322 helix: 0.90 (0.18), residues: 878 sheet: -0.52 (0.96), residues: 36 loop : -2.10 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS B 723 PHE 0.018 0.001 PHE A 385 TYR 0.023 0.002 TYR A 361 ARG 0.010 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2838.37 seconds wall clock time: 52 minutes 27.51 seconds (3147.51 seconds total)