Starting phenix.real_space_refine on Wed Feb 12 13:20:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ln5_0924/02_2025/6ln5_0924.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ln5_0924/02_2025/6ln5_0924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ln5_0924/02_2025/6ln5_0924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ln5_0924/02_2025/6ln5_0924.map" model { file = "/net/cci-nas-00/data/ceres_data/6ln5_0924/02_2025/6ln5_0924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ln5_0924/02_2025/6ln5_0924.cif" } resolution = 2.8 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= 0.000 sd= 0.011 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 4988 2.51 5 N 1311 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7840 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7806 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 46, 'TRANS': 964} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.67, per 1000 atoms: 0.60 Number of scatterers: 7840 At special positions: 0 Unit cell: (103.335, 79.68, 138.195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 57 16.00 P 3 15.00 Mg 1 11.99 O 1478 8.00 N 1311 7.00 C 4988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.02 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: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 7 sheets defined 53.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.686A pdb=" N VAL A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.955A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 118 removed outlier: 3.500A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.731A pdb=" N THR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 275 removed outlier: 3.545A pdb=" N LYS A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 287 through 307 Processing helix chain 'A' and resid 310 through 329 removed outlier: 3.614A pdb=" N THR A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.405A pdb=" N VAL A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.828A pdb=" N GLN A 406 " --> pdb=" O ASN A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.833A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 516 through 523 Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.556A pdb=" N LYS A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.539A pdb=" N TYR A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 4.322A pdb=" N ALA A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 670 removed outlier: 3.732A pdb=" N ASP A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 692 removed outlier: 3.626A pdb=" N SER A 684 " --> pdb=" O PRO A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 739 through 781 removed outlier: 4.252A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 799 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 806 through 809 Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.637A pdb=" N TYR A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 854 " --> pdb=" O ALA A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 872 through 875 removed outlier: 3.601A pdb=" N CYS A 875 " --> pdb=" O PHE A 872 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 872 through 875' Processing helix chain 'A' and resid 888 through 891 removed outlier: 3.585A pdb=" N GLU A 891 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 891' Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.447A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 913 " --> pdb=" O CYS A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 Processing helix chain 'A' and resid 929 through 949 Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.791A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1031 Proline residue: A1024 - end of helix removed outlier: 3.593A pdb=" N TRP A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.366A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 222 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LEU A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 224 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE A 163 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.700A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP A 176 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE A 214 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333 removed outlier: 6.121A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 652 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.597A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.868A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.601A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 14.859A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.597A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.868A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.601A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 14.859A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ARG A 371 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 590 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY A 594 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER A 493 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU A 486 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER A 495 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 484 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A 497 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.597A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.554A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 16.501A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER A 493 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU A 486 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N SER A 495 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR A 484 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TYR A 497 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 428 433 hydrogen bonds defined for protein. 1257 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: 3.59 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2575 1.35 - 1.48: 1793 1.48 - 1.61: 3523 1.61 - 1.73: 4 1.73 - 1.86: 90 Bond restraints: 7985 Sorted by residual: bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.618 -0.228 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.307 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C4' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.428 1.302 0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 1.335 1.449 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C2' ACP A2001 " pdb=" O2' ACP A2001 " ideal model delta sigma weight residual 1.401 1.493 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 7980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 10792 3.11 - 6.22: 43 6.22 - 9.33: 3 9.33 - 12.44: 5 12.44 - 15.54: 1 Bond angle restraints: 10844 Sorted by residual: angle pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O5' ACP A2001 " ideal model delta sigma weight residual 93.75 109.29 -15.54 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C3B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O3A ACP A2001 " ideal model delta sigma weight residual 98.05 110.00 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N1 ACP A2001 " pdb=" C6 ACP A2001 " pdb=" N6 ACP A2001 " ideal model delta sigma weight residual 119.32 108.11 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" O1B ACP A2001 " pdb=" PB ACP A2001 " pdb=" O2B ACP A2001 " ideal model delta sigma weight residual 119.60 109.01 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1A ACP A2001 " pdb=" PA ACP A2001 " pdb=" O2A ACP A2001 " ideal model delta sigma weight residual 118.95 108.61 10.34 3.00e+00 1.11e-01 1.19e+01 ... (remaining 10839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 4614 21.94 - 43.89: 215 43.89 - 65.83: 16 65.83 - 87.78: 14 87.78 - 109.72: 2 Dihedral angle restraints: 4861 sinusoidal: 1941 harmonic: 2920 Sorted by residual: dihedral pdb=" CA CYS A 887 " pdb=" C CYS A 887 " pdb=" N ALA A 888 " pdb=" CA ALA A 888 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" O1A ACP A2001 " pdb=" O3A ACP A2001 " pdb=" PA ACP A2001 " pdb=" PB ACP A2001 " ideal model delta sinusoidal sigma weight residual -48.75 60.97 -109.72 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CA PRO A 951 " pdb=" C PRO A 951 " pdb=" N LEU A 952 " pdb=" CA LEU A 952 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1177 0.077 - 0.154: 95 0.154 - 0.231: 0 0.231 - 0.308: 0 0.308 - 0.385: 1 Chirality restraints: 1273 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.37 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL A 437 " pdb=" N VAL A 437 " pdb=" C VAL A 437 " pdb=" CB VAL A 437 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1270 not shown) Planarity restraints: 1377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1016 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A1017 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A1017 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1017 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 975 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 787 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 788 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 788 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 788 " 0.020 5.00e-02 4.00e+02 ... (remaining 1374 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 74 2.60 - 3.18: 6618 3.18 - 3.75: 12044 3.75 - 4.33: 17696 4.33 - 4.90: 29002 Nonbonded interactions: 65434 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.027 2.170 nonbonded pdb=" OE2 GLU A 309 " pdb=" OD1 ASN A 795 " model vdw 2.027 3.040 nonbonded pdb=" O ILE A 307 " pdb=" OE1 GLU A 309 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.172 2.170 nonbonded pdb=" NH1 ARG A 491 " pdb=" OE2 GLU A 587 " model vdw 2.212 3.120 ... (remaining 65429 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 7985 Z= 0.335 Angle : 0.630 15.544 10844 Z= 0.335 Chirality : 0.042 0.385 1273 Planarity : 0.004 0.039 1377 Dihedral : 12.833 109.724 2966 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.16 (0.20), residues: 1007 helix: -3.50 (0.13), residues: 500 sheet: -1.77 (0.40), residues: 132 loop : -1.65 (0.27), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 793 HIS 0.006 0.001 HIS A 566 PHE 0.011 0.001 PHE A 367 TYR 0.007 0.001 TYR A 295 ARG 0.002 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.905 Fit side-chains REVERT: A 30 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7435 (tttm) REVERT: A 31 LYS cc_start: 0.7380 (mttt) cc_final: 0.7128 (mmtp) REVERT: A 33 LYS cc_start: 0.7988 (tptm) cc_final: 0.7734 (tppt) REVERT: A 135 LYS cc_start: 0.7602 (pttt) cc_final: 0.7264 (mmtp) REVERT: A 143 LYS cc_start: 0.8190 (pttt) cc_final: 0.7820 (ptmt) REVERT: A 153 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8281 (tt) REVERT: A 259 GLN cc_start: 0.8079 (mt0) cc_final: 0.7770 (mt0) REVERT: A 365 ARG cc_start: 0.8105 (ptp-170) cc_final: 0.7899 (ptm160) REVERT: A 371 ARG cc_start: 0.6508 (ptp-110) cc_final: 0.6069 (ptp90) REVERT: A 379 LEU cc_start: 0.8347 (mt) cc_final: 0.8115 (mp) REVERT: A 387 SER cc_start: 0.8261 (p) cc_final: 0.8047 (p) REVERT: A 397 LYS cc_start: 0.7505 (tptp) cc_final: 0.7238 (tmtt) REVERT: A 431 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8139 (mttp) REVERT: A 433 VAL cc_start: 0.8698 (p) cc_final: 0.8447 (m) REVERT: A 510 LYS cc_start: 0.8237 (mttt) cc_final: 0.8031 (mtpp) REVERT: A 541 LYS cc_start: 0.8815 (tttt) cc_final: 0.8578 (ttmt) REVERT: A 549 ARG cc_start: 0.7035 (mtt180) cc_final: 0.6561 (mtm110) REVERT: A 568 ASN cc_start: 0.8016 (m110) cc_final: 0.7636 (m-40) REVERT: A 582 ASN cc_start: 0.7674 (m-40) cc_final: 0.7113 (m-40) REVERT: A 585 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7734 (mttt) REVERT: A 719 MET cc_start: 0.8879 (mmm) cc_final: 0.8209 (mmt) REVERT: A 896 MET cc_start: 0.8490 (mtp) cc_final: 0.8008 (mtm) REVERT: A 968 MET cc_start: 0.8225 (tpt) cc_final: 0.7933 (mmm) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 1.4597 time to fit residues: 256.0166 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 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 3 ASN A 284 HIS A 643 GLN A 874 GLN A 913 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105831 restraints weight = 8951.535| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.67 r_work: 0.3010 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7985 Z= 0.165 Angle : 0.508 6.037 10844 Z= 0.266 Chirality : 0.041 0.129 1273 Planarity : 0.005 0.040 1377 Dihedral : 8.318 148.578 1107 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.55 % Allowed : 9.84 % Favored : 87.62 % 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: -1.40 (0.24), residues: 1007 helix: -0.64 (0.21), residues: 508 sheet: -1.00 (0.46), residues: 122 loop : -1.07 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.002 0.001 HIS A 396 PHE 0.012 0.001 PHE A 367 TYR 0.010 0.001 TYR A 842 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.868 Fit side-chains REVERT: A 20 GLU cc_start: 0.7918 (pt0) cc_final: 0.7703 (pt0) REVERT: A 31 LYS cc_start: 0.7623 (mttt) cc_final: 0.7139 (mmtp) REVERT: A 77 TRP cc_start: 0.7951 (t60) cc_final: 0.7730 (t-100) REVERT: A 135 LYS cc_start: 0.7870 (pttt) cc_final: 0.7299 (mmtp) REVERT: A 174 ARG cc_start: 0.8252 (mtt-85) cc_final: 0.7804 (mtt-85) REVERT: A 239 MET cc_start: 0.5379 (mtt) cc_final: 0.4033 (tpt) REVERT: A 370 ASP cc_start: 0.6769 (t0) cc_final: 0.6481 (t0) REVERT: A 371 ARG cc_start: 0.6785 (ptp-110) cc_final: 0.6123 (ptp90) REVERT: A 397 LYS cc_start: 0.7699 (tptp) cc_final: 0.7424 (tmtt) REVERT: A 431 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8372 (mttp) REVERT: A 510 LYS cc_start: 0.8393 (mttt) cc_final: 0.8109 (mtpp) REVERT: A 518 GLU cc_start: 0.8042 (mp0) cc_final: 0.7562 (mt-10) REVERT: A 541 LYS cc_start: 0.8593 (tttt) cc_final: 0.8196 (ttmt) REVERT: A 549 ARG cc_start: 0.7671 (mtt180) cc_final: 0.6896 (ttp-110) REVERT: A 568 ASN cc_start: 0.8002 (m110) cc_final: 0.7696 (m-40) REVERT: A 585 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7812 (mttt) REVERT: A 719 MET cc_start: 0.9168 (mmm) cc_final: 0.8603 (mmt) REVERT: A 797 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8117 (p) REVERT: A 896 MET cc_start: 0.8960 (mtp) cc_final: 0.8522 (mtm) REVERT: A 917 GLU cc_start: 0.8363 (tt0) cc_final: 0.7812 (tp30) REVERT: A 968 MET cc_start: 0.8302 (tpt) cc_final: 0.7888 (mmm) outliers start: 22 outliers final: 8 residues processed: 148 average time/residue: 1.4141 time to fit residues: 220.4003 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN A 643 GLN A 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105498 restraints weight = 8981.968| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.56 r_work: 0.3019 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7985 Z= 0.230 Angle : 0.526 5.762 10844 Z= 0.271 Chirality : 0.043 0.134 1273 Planarity : 0.004 0.037 1377 Dihedral : 8.618 158.904 1107 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.66 % Allowed : 14.12 % Favored : 83.22 % 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: -0.36 (0.25), residues: 1007 helix: 0.40 (0.23), residues: 510 sheet: -0.95 (0.46), residues: 119 loop : -0.72 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1016 HIS 0.002 0.001 HIS A 15 PHE 0.014 0.001 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.004 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.992 Fit side-chains REVERT: A 20 GLU cc_start: 0.7950 (pt0) cc_final: 0.7734 (pt0) REVERT: A 31 LYS cc_start: 0.7627 (mttt) cc_final: 0.7167 (mmtp) REVERT: A 77 TRP cc_start: 0.8008 (t60) cc_final: 0.7806 (t-100) REVERT: A 135 LYS cc_start: 0.7795 (pttt) cc_final: 0.7238 (mmtp) REVERT: A 239 MET cc_start: 0.5295 (mtt) cc_final: 0.4094 (tpt) REVERT: A 370 ASP cc_start: 0.6820 (t0) cc_final: 0.6566 (t0) REVERT: A 371 ARG cc_start: 0.6717 (ptp-110) cc_final: 0.6039 (ptp90) REVERT: A 397 LYS cc_start: 0.7926 (tptp) cc_final: 0.7442 (tmtt) REVERT: A 431 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8457 (mttp) REVERT: A 510 LYS cc_start: 0.8442 (mttt) cc_final: 0.8178 (mtpp) REVERT: A 528 ARG cc_start: 0.8758 (tpp-160) cc_final: 0.8509 (tpp-160) REVERT: A 541 LYS cc_start: 0.8632 (tttt) cc_final: 0.8373 (ttmt) REVERT: A 549 ARG cc_start: 0.7708 (mtt180) cc_final: 0.6967 (ttp-110) REVERT: A 568 ASN cc_start: 0.8003 (m110) cc_final: 0.7677 (m-40) REVERT: A 585 LYS cc_start: 0.8404 (mtpp) cc_final: 0.7952 (mttt) REVERT: A 714 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: A 719 MET cc_start: 0.9192 (mmm) cc_final: 0.8644 (mmt) REVERT: A 797 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8261 (p) REVERT: A 896 MET cc_start: 0.8929 (mtp) cc_final: 0.8529 (mtm) REVERT: A 989 ASN cc_start: 0.8090 (m-40) cc_final: 0.7870 (m-40) outliers start: 23 outliers final: 13 residues processed: 138 average time/residue: 1.4463 time to fit residues: 210.2592 Evaluate side-chains 130 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 GLN A 874 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104528 restraints weight = 8917.642| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.54 r_work: 0.3018 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7985 Z= 0.250 Angle : 0.539 6.019 10844 Z= 0.276 Chirality : 0.043 0.135 1273 Planarity : 0.004 0.036 1377 Dihedral : 8.854 165.131 1107 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.59 % Allowed : 14.12 % Favored : 82.29 % 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: 0.11 (0.26), residues: 1007 helix: 0.84 (0.23), residues: 509 sheet: -0.63 (0.45), residues: 129 loop : -0.61 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1016 HIS 0.003 0.001 HIS A 15 PHE 0.016 0.001 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.003 0.001 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.940 Fit side-chains REVERT: A 20 GLU cc_start: 0.7924 (pt0) cc_final: 0.7685 (pt0) REVERT: A 27 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: A 31 LYS cc_start: 0.7642 (mttt) cc_final: 0.7138 (mmtp) REVERT: A 77 TRP cc_start: 0.8018 (t60) cc_final: 0.7711 (t-100) REVERT: A 135 LYS cc_start: 0.7927 (pttt) cc_final: 0.7381 (mmtp) REVERT: A 143 LYS cc_start: 0.8563 (pttt) cc_final: 0.8182 (ptmt) REVERT: A 239 MET cc_start: 0.5259 (mtt) cc_final: 0.4069 (tpt) REVERT: A 370 ASP cc_start: 0.6836 (t0) cc_final: 0.6584 (t0) REVERT: A 371 ARG cc_start: 0.6525 (ptp-110) cc_final: 0.5856 (ptp90) REVERT: A 397 LYS cc_start: 0.7968 (tptp) cc_final: 0.7548 (tmtt) REVERT: A 406 GLN cc_start: 0.7032 (mp10) cc_final: 0.6803 (mp10) REVERT: A 431 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8485 (mttp) REVERT: A 510 LYS cc_start: 0.8362 (mttt) cc_final: 0.8132 (mtpp) REVERT: A 528 ARG cc_start: 0.8777 (tpp-160) cc_final: 0.8213 (tpp-160) REVERT: A 529 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8216 (m) REVERT: A 541 LYS cc_start: 0.8665 (tttt) cc_final: 0.8371 (ttmt) REVERT: A 549 ARG cc_start: 0.7672 (mtt180) cc_final: 0.6975 (ttp-110) REVERT: A 585 LYS cc_start: 0.8442 (mtpp) cc_final: 0.7992 (mttt) REVERT: A 604 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8130 (mm) REVERT: A 719 MET cc_start: 0.9213 (mmm) cc_final: 0.8679 (mmt) REVERT: A 797 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8388 (p) REVERT: A 896 MET cc_start: 0.8931 (mtp) cc_final: 0.8570 (mtm) REVERT: A 989 ASN cc_start: 0.8095 (m-40) cc_final: 0.7866 (m-40) outliers start: 31 outliers final: 16 residues processed: 134 average time/residue: 1.4033 time to fit residues: 198.2036 Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 86 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106001 restraints weight = 8818.702| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.57 r_work: 0.2985 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7985 Z= 0.155 Angle : 0.491 5.739 10844 Z= 0.251 Chirality : 0.041 0.125 1273 Planarity : 0.004 0.033 1377 Dihedral : 8.707 163.472 1107 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.78 % Allowed : 15.28 % Favored : 81.94 % 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: 0.55 (0.27), residues: 1007 helix: 1.23 (0.24), residues: 509 sheet: -0.67 (0.46), residues: 119 loop : -0.35 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 793 HIS 0.002 0.000 HIS A 15 PHE 0.015 0.001 PHE A 367 TYR 0.012 0.001 TYR A 295 ARG 0.005 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.895 Fit side-chains REVERT: A 20 GLU cc_start: 0.7915 (pt0) cc_final: 0.7660 (pt0) REVERT: A 31 LYS cc_start: 0.7572 (mttt) cc_final: 0.7126 (mmtp) REVERT: A 65 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8087 (mp) REVERT: A 77 TRP cc_start: 0.7974 (t60) cc_final: 0.7675 (t-100) REVERT: A 135 LYS cc_start: 0.7905 (pttt) cc_final: 0.7278 (mmtp) REVERT: A 207 MET cc_start: 0.9063 (mmm) cc_final: 0.8836 (tpp) REVERT: A 239 MET cc_start: 0.5250 (mtt) cc_final: 0.3919 (tpt) REVERT: A 361 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8200 (mtm) REVERT: A 371 ARG cc_start: 0.6412 (ptp-110) cc_final: 0.5765 (ptp90) REVERT: A 397 LYS cc_start: 0.7935 (tptp) cc_final: 0.7477 (tmtt) REVERT: A 431 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8474 (mttp) REVERT: A 510 LYS cc_start: 0.8243 (mttt) cc_final: 0.8003 (mtpp) REVERT: A 528 ARG cc_start: 0.8742 (tpp-160) cc_final: 0.8169 (tpp-160) REVERT: A 541 LYS cc_start: 0.8560 (tttt) cc_final: 0.8327 (ttmt) REVERT: A 549 ARG cc_start: 0.7651 (mtt180) cc_final: 0.6997 (mtp180) REVERT: A 585 LYS cc_start: 0.8399 (mtpp) cc_final: 0.7811 (mttt) REVERT: A 719 MET cc_start: 0.9149 (mmm) cc_final: 0.8701 (mmp) REVERT: A 797 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8146 (p) REVERT: A 891 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: A 896 MET cc_start: 0.8935 (mtp) cc_final: 0.8597 (mtm) REVERT: A 989 ASN cc_start: 0.8137 (m-40) cc_final: 0.7891 (m-40) outliers start: 24 outliers final: 10 residues processed: 133 average time/residue: 1.4012 time to fit residues: 196.3101 Evaluate side-chains 120 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105823 restraints weight = 8841.315| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.52 r_work: 0.2949 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7985 Z= 0.225 Angle : 0.530 6.151 10844 Z= 0.270 Chirality : 0.043 0.133 1273 Planarity : 0.004 0.035 1377 Dihedral : 8.739 164.717 1107 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.24 % Allowed : 15.62 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.27), residues: 1007 helix: 1.25 (0.24), residues: 509 sheet: -0.44 (0.45), residues: 129 loop : -0.35 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.003 0.001 HIS A 15 PHE 0.014 0.001 PHE A 367 TYR 0.015 0.001 TYR A 842 ARG 0.004 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.916 Fit side-chains REVERT: A 20 GLU cc_start: 0.7910 (pt0) cc_final: 0.7661 (pt0) REVERT: A 31 LYS cc_start: 0.7606 (mttt) cc_final: 0.7159 (mmtp) REVERT: A 65 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8124 (mp) REVERT: A 77 TRP cc_start: 0.8017 (t60) cc_final: 0.7732 (t-100) REVERT: A 135 LYS cc_start: 0.7896 (pttt) cc_final: 0.7354 (mmtp) REVERT: A 143 LYS cc_start: 0.8562 (pttt) cc_final: 0.8171 (ptmt) REVERT: A 207 MET cc_start: 0.9124 (mmm) cc_final: 0.8866 (tpp) REVERT: A 239 MET cc_start: 0.5208 (mtt) cc_final: 0.4017 (tpt) REVERT: A 361 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: A 371 ARG cc_start: 0.6246 (ptp-110) cc_final: 0.5703 (ptp90) REVERT: A 397 LYS cc_start: 0.7966 (tptp) cc_final: 0.7487 (tmtt) REVERT: A 398 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: A 431 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8488 (mttp) REVERT: A 467 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7678 (mtt90) REVERT: A 506 THR cc_start: 0.3071 (OUTLIER) cc_final: 0.2787 (t) REVERT: A 510 LYS cc_start: 0.8268 (mttt) cc_final: 0.8030 (mtpp) REVERT: A 528 ARG cc_start: 0.8723 (tpp-160) cc_final: 0.8197 (tpp-160) REVERT: A 541 LYS cc_start: 0.8565 (tttt) cc_final: 0.8281 (ttmt) REVERT: A 549 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7054 (mtp180) REVERT: A 585 LYS cc_start: 0.8405 (mtpp) cc_final: 0.7796 (mttt) REVERT: A 719 MET cc_start: 0.9187 (mmm) cc_final: 0.8688 (mmt) REVERT: A 797 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8352 (p) REVERT: A 891 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: A 896 MET cc_start: 0.8939 (mtp) cc_final: 0.8634 (mtm) REVERT: A 989 ASN cc_start: 0.8097 (m-40) cc_final: 0.7871 (m-40) outliers start: 28 outliers final: 15 residues processed: 131 average time/residue: 1.4513 time to fit residues: 200.2920 Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.106206 restraints weight = 8882.441| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.52 r_work: 0.2967 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7985 Z= 0.189 Angle : 0.514 6.498 10844 Z= 0.261 Chirality : 0.042 0.129 1273 Planarity : 0.004 0.033 1377 Dihedral : 8.692 164.602 1107 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.24 % Allowed : 16.32 % Favored : 80.44 % 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: 0.72 (0.27), residues: 1007 helix: 1.35 (0.24), residues: 509 sheet: -0.35 (0.44), residues: 134 loop : -0.32 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1016 HIS 0.002 0.001 HIS A 15 PHE 0.014 0.001 PHE A 367 TYR 0.013 0.001 TYR A 295 ARG 0.004 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.950 Fit side-chains REVERT: A 20 GLU cc_start: 0.7900 (pt0) cc_final: 0.7645 (pt0) REVERT: A 27 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7185 (tp30) REVERT: A 65 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8133 (mp) REVERT: A 77 TRP cc_start: 0.8113 (t60) cc_final: 0.7665 (t-100) REVERT: A 135 LYS cc_start: 0.7846 (pttt) cc_final: 0.7322 (mmtp) REVERT: A 143 LYS cc_start: 0.8558 (pttt) cc_final: 0.8166 (ptmt) REVERT: A 207 MET cc_start: 0.9141 (mmm) cc_final: 0.8900 (tpp) REVERT: A 239 MET cc_start: 0.5251 (mtt) cc_final: 0.3904 (tpt) REVERT: A 361 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8332 (mtm) REVERT: A 371 ARG cc_start: 0.6389 (ptp-110) cc_final: 0.5897 (ptp90) REVERT: A 397 LYS cc_start: 0.7974 (tptp) cc_final: 0.7490 (tmtt) REVERT: A 398 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6488 (m-30) REVERT: A 431 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8507 (mttp) REVERT: A 467 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7757 (mtt90) REVERT: A 506 THR cc_start: 0.2978 (OUTLIER) cc_final: 0.2740 (t) REVERT: A 510 LYS cc_start: 0.8314 (mttt) cc_final: 0.8073 (mtpp) REVERT: A 528 ARG cc_start: 0.8692 (tpp-160) cc_final: 0.8178 (tpp-160) REVERT: A 541 LYS cc_start: 0.8567 (tttt) cc_final: 0.8245 (ttmt) REVERT: A 549 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7056 (mtp180) REVERT: A 568 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.8024 (m-40) REVERT: A 585 LYS cc_start: 0.8532 (mtpp) cc_final: 0.7877 (mttt) REVERT: A 719 MET cc_start: 0.9168 (mmm) cc_final: 0.8683 (mmt) REVERT: A 797 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8243 (p) REVERT: A 891 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: A 896 MET cc_start: 0.8939 (mtp) cc_final: 0.8629 (mtm) REVERT: A 989 ASN cc_start: 0.8090 (m-40) cc_final: 0.7862 (m-40) outliers start: 28 outliers final: 15 residues processed: 130 average time/residue: 1.5086 time to fit residues: 206.1777 Evaluate side-chains 129 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104104 restraints weight = 8963.565| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.55 r_work: 0.2945 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7985 Z= 0.233 Angle : 0.545 6.855 10844 Z= 0.275 Chirality : 0.043 0.134 1273 Planarity : 0.004 0.035 1377 Dihedral : 8.857 167.967 1107 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.47 % Allowed : 16.44 % Favored : 80.09 % 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: 0.69 (0.27), residues: 1007 helix: 1.30 (0.24), residues: 509 sheet: -0.34 (0.45), residues: 134 loop : -0.30 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.003 0.001 HIS A 15 PHE 0.014 0.001 PHE A 367 TYR 0.015 0.002 TYR A 842 ARG 0.004 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.879 Fit side-chains REVERT: A 20 GLU cc_start: 0.7979 (pt0) cc_final: 0.7731 (pt0) REVERT: A 31 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7335 (mmtp) REVERT: A 65 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8123 (mp) REVERT: A 77 TRP cc_start: 0.8217 (t60) cc_final: 0.7713 (t-100) REVERT: A 135 LYS cc_start: 0.7857 (pttt) cc_final: 0.7327 (mmtp) REVERT: A 143 LYS cc_start: 0.8580 (pttt) cc_final: 0.8154 (ptmt) REVERT: A 207 MET cc_start: 0.9128 (mmm) cc_final: 0.8867 (tpp) REVERT: A 239 MET cc_start: 0.5195 (mtt) cc_final: 0.4011 (tpt) REVERT: A 361 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.8395 (mtm) REVERT: A 371 ARG cc_start: 0.6483 (ptp-110) cc_final: 0.6028 (ptp90) REVERT: A 397 LYS cc_start: 0.7992 (tptp) cc_final: 0.7492 (tmtt) REVERT: A 398 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6392 (m-30) REVERT: A 431 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8466 (mttp) REVERT: A 462 LEU cc_start: 0.8109 (mt) cc_final: 0.7827 (mt) REVERT: A 467 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7725 (mtt90) REVERT: A 506 THR cc_start: 0.3055 (OUTLIER) cc_final: 0.2778 (t) REVERT: A 510 LYS cc_start: 0.8291 (mttt) cc_final: 0.8053 (mtpp) REVERT: A 528 ARG cc_start: 0.8751 (tpp-160) cc_final: 0.8219 (tpp-160) REVERT: A 541 LYS cc_start: 0.8537 (tttt) cc_final: 0.8228 (ttmt) REVERT: A 549 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7078 (mtp180) REVERT: A 585 LYS cc_start: 0.8464 (mtpp) cc_final: 0.7804 (mttt) REVERT: A 719 MET cc_start: 0.9194 (mmm) cc_final: 0.8758 (mmt) REVERT: A 797 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8368 (p) REVERT: A 891 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: A 896 MET cc_start: 0.8925 (mtp) cc_final: 0.8618 (mtm) REVERT: A 989 ASN cc_start: 0.8113 (m-40) cc_final: 0.7877 (m-40) outliers start: 30 outliers final: 18 residues processed: 134 average time/residue: 1.4210 time to fit residues: 200.5469 Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 0.0020 chunk 15 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.135027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106753 restraints weight = 9112.268| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.53 r_work: 0.3082 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7985 Z= 0.195 Angle : 0.527 7.134 10844 Z= 0.265 Chirality : 0.042 0.129 1273 Planarity : 0.004 0.033 1377 Dihedral : 8.766 166.632 1107 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.78 % Allowed : 16.90 % Favored : 80.32 % 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: 0.79 (0.27), residues: 1007 helix: 1.38 (0.24), residues: 510 sheet: -0.33 (0.44), residues: 134 loop : -0.23 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1016 HIS 0.002 0.001 HIS A 15 PHE 0.015 0.001 PHE A 73 TYR 0.013 0.001 TYR A 295 ARG 0.005 0.000 ARG A 923 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.885 Fit side-chains REVERT: A 20 GLU cc_start: 0.7938 (pt0) cc_final: 0.7701 (pt0) REVERT: A 31 LYS cc_start: 0.8323 (mtmm) cc_final: 0.7380 (mmtp) REVERT: A 65 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 77 TRP cc_start: 0.8240 (t60) cc_final: 0.7767 (t-100) REVERT: A 135 LYS cc_start: 0.7810 (pttt) cc_final: 0.7298 (mmtp) REVERT: A 143 LYS cc_start: 0.8572 (pttt) cc_final: 0.8151 (ptmt) REVERT: A 207 MET cc_start: 0.9156 (mmm) cc_final: 0.8906 (tpp) REVERT: A 239 MET cc_start: 0.5250 (mtt) cc_final: 0.3918 (tpt) REVERT: A 361 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8361 (mtm) REVERT: A 371 ARG cc_start: 0.6314 (ptp-110) cc_final: 0.5886 (ptp90) REVERT: A 397 LYS cc_start: 0.7989 (tptp) cc_final: 0.7495 (tmtt) REVERT: A 431 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8513 (mttp) REVERT: A 462 LEU cc_start: 0.8152 (mt) cc_final: 0.7857 (mt) REVERT: A 467 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7777 (mtt90) REVERT: A 506 THR cc_start: 0.2972 (OUTLIER) cc_final: 0.2733 (t) REVERT: A 510 LYS cc_start: 0.8342 (mttt) cc_final: 0.8103 (mttm) REVERT: A 541 LYS cc_start: 0.8548 (tttt) cc_final: 0.8247 (ttmt) REVERT: A 549 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7074 (mtp180) REVERT: A 585 LYS cc_start: 0.8520 (mtpp) cc_final: 0.7860 (mttt) REVERT: A 719 MET cc_start: 0.9166 (mmm) cc_final: 0.8737 (mmt) REVERT: A 797 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8375 (p) REVERT: A 891 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: A 896 MET cc_start: 0.8923 (mtp) cc_final: 0.8610 (mtm) REVERT: A 989 ASN cc_start: 0.8081 (m-40) cc_final: 0.7850 (m-40) outliers start: 24 outliers final: 17 residues processed: 128 average time/residue: 1.4642 time to fit residues: 197.3474 Evaluate side-chains 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.136640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108459 restraints weight = 8983.472| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.55 r_work: 0.3062 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7985 Z= 0.168 Angle : 0.517 7.334 10844 Z= 0.259 Chirality : 0.041 0.127 1273 Planarity : 0.004 0.032 1377 Dihedral : 8.629 165.004 1107 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.43 % Allowed : 17.71 % Favored : 79.86 % 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: 0.90 (0.27), residues: 1007 helix: 1.46 (0.24), residues: 513 sheet: -0.31 (0.44), residues: 134 loop : -0.19 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 PHE 0.015 0.001 PHE A 73 TYR 0.012 0.001 TYR A 842 ARG 0.005 0.000 ARG A 923 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.910 Fit side-chains REVERT: A 20 GLU cc_start: 0.7966 (pt0) cc_final: 0.7734 (pt0) REVERT: A 31 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7492 (mmtp) REVERT: A 65 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 77 TRP cc_start: 0.8267 (t60) cc_final: 0.7804 (t-100) REVERT: A 135 LYS cc_start: 0.7863 (pttt) cc_final: 0.7438 (mmtp) REVERT: A 239 MET cc_start: 0.5308 (mtt) cc_final: 0.3926 (tpt) REVERT: A 361 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8398 (mtm) REVERT: A 371 ARG cc_start: 0.6456 (ptp-110) cc_final: 0.6164 (ptp90) REVERT: A 397 LYS cc_start: 0.8038 (tptp) cc_final: 0.7588 (tmtt) REVERT: A 431 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8569 (mttp) REVERT: A 462 LEU cc_start: 0.8222 (mt) cc_final: 0.7783 (mm) REVERT: A 506 THR cc_start: 0.2791 (OUTLIER) cc_final: 0.2581 (t) REVERT: A 510 LYS cc_start: 0.8413 (mttt) cc_final: 0.8196 (mttm) REVERT: A 541 LYS cc_start: 0.8609 (tttt) cc_final: 0.8315 (ttmt) REVERT: A 549 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7126 (mtp180) REVERT: A 585 LYS cc_start: 0.8582 (mtpp) cc_final: 0.7892 (mttt) REVERT: A 719 MET cc_start: 0.9185 (mmm) cc_final: 0.8594 (mmt) REVERT: A 797 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 891 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: A 896 MET cc_start: 0.8956 (mtp) cc_final: 0.8688 (mtm) REVERT: A 989 ASN cc_start: 0.8147 (m-40) cc_final: 0.7907 (m-40) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 1.3951 time to fit residues: 179.3072 Evaluate side-chains 122 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 891 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 85 optimal weight: 0.0970 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109784 restraints weight = 8894.872| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.49 r_work: 0.3091 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7985 Z= 0.164 Angle : 0.516 8.203 10844 Z= 0.257 Chirality : 0.041 0.127 1273 Planarity : 0.004 0.033 1377 Dihedral : 8.532 162.398 1107 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.55 % Allowed : 17.82 % Favored : 79.63 % 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: 0.99 (0.27), residues: 1007 helix: 1.50 (0.24), residues: 515 sheet: -0.24 (0.45), residues: 134 loop : -0.10 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.002 0.001 HIS A 15 PHE 0.014 0.001 PHE A 73 TYR 0.012 0.001 TYR A 842 ARG 0.006 0.000 ARG A 923 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6325.82 seconds wall clock time: 112 minutes 5.90 seconds (6725.90 seconds total)