Starting phenix.real_space_refine on Fri Sep 11 05:24:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ln5_0924/09_2026/6ln5_0924.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ln5_0924/09_2026/6ln5_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6ln5_0924/09_2026/6ln5_0924.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ln5_0924/09_2026/6ln5_0924.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ln5_0924/09_2026/6ln5_0924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ln5_0924/09_2026/6ln5_0924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ln5_0924/09_2026/6ln5_0924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ln5_0924/09_2026/6ln5_0924.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 1.95, per 1000 atoms: 0.25 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: 0.72 Conformation dependent library (CDL) restraints added in 430.1 milliseconds 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: 0.29 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: 1.44 Time building geometry restraints manager: 0.96 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: 4603 21.94 - 43.89: 205 43.89 - 65.83: 13 65.83 - 87.78: 10 87.78 - 109.72: 2 Dihedral angle restraints: 4833 sinusoidal: 1913 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 4830 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: 0.430 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.070 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 7986 Z= 0.258 Angle : 0.630 15.544 10846 Z= 0.335 Chirality : 0.042 0.385 1273 Planarity : 0.004 0.039 1377 Dihedral : 12.322 109.724 2938 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (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 ARG 0.002 0.000 ARG A 467 TYR 0.007 0.001 TYR A 295 PHE 0.011 0.001 PHE A 367 TRP 0.006 0.001 TRP A 793 HIS 0.006 0.001 HIS A 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 ( 7985) covalent geometry : angle 0.63001 / 0.34 (10844) SS BOND : bond 0.00729 / 0.38 ( 1) SS BOND : angle 0.52288 / 0.29 ( 2) hydrogen bonds : bond 0.26214 / 17.06 ( 399) hydrogen bonds : angle 8.91264 / 6.15 ( 1257) *********************** 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 : 0.322 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: 0.8238 (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: 0.7932 (mmm) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.6755 time to fit residues: 118.4119 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 : 0.256 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 HIS A 469 ASN A 643 GLN A 874 GLN A 913 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105554 restraints weight = 9034.067| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.68 r_work: 0.3004 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7986 Z= 0.119 Angle : 0.510 6.103 10846 Z= 0.268 Chirality : 0.041 0.130 1273 Planarity : 0.005 0.039 1377 Dihedral : 6.548 136.987 1079 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.24), residues: 1007 helix: -0.63 (0.21), residues: 508 sheet: -0.99 (0.46), residues: 122 loop : -1.07 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.010 0.001 TYR A 295 PHE 0.013 0.001 PHE A 367 TRP 0.009 0.001 TRP A1016 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7985) covalent geometry : angle 0.51002 / 0.27 (10844) SS BOND : bond 0.00561 / 0.30 ( 1) SS BOND : angle 0.69241 / 0.39 ( 2) hydrogen bonds : bond 0.04477 / 2.92 ( 399) hydrogen bonds : angle 4.68224 / 3.29 ( 1257) *********************** 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 155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.276 Fit side-chains REVERT: A 20 GLU cc_start: 0.7923 (pt0) cc_final: 0.7704 (pt0) REVERT: A 31 LYS cc_start: 0.7626 (mttt) cc_final: 0.7144 (mmtp) REVERT: A 77 TRP cc_start: 0.7946 (t60) cc_final: 0.7727 (t-100) REVERT: A 135 LYS cc_start: 0.7883 (pttt) cc_final: 0.7305 (mmtp) REVERT: A 174 ARG cc_start: 0.8259 (mtt-85) cc_final: 0.7807 (mtt-85) REVERT: A 239 MET cc_start: 0.5381 (mtt) cc_final: 0.4029 (tpt) REVERT: A 370 ASP cc_start: 0.6768 (t0) cc_final: 0.6465 (t0) REVERT: A 371 ARG cc_start: 0.6758 (ptp-110) cc_final: 0.6078 (ptp90) REVERT: A 397 LYS cc_start: 0.7793 (tptp) cc_final: 0.7493 (tmtt) REVERT: A 431 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8373 (mttp) REVERT: A 510 LYS cc_start: 0.8388 (mttt) cc_final: 0.8104 (mtpp) REVERT: A 541 LYS cc_start: 0.8588 (tttt) cc_final: 0.8186 (ttmt) REVERT: A 549 ARG cc_start: 0.7696 (mtt180) cc_final: 0.6899 (ttp-110) REVERT: A 568 ASN cc_start: 0.8005 (m110) cc_final: 0.7702 (m-40) REVERT: A 585 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7815 (mttt) REVERT: A 719 MET cc_start: 0.9155 (mmm) cc_final: 0.8599 (mmt) REVERT: A 797 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8124 (p) REVERT: A 896 MET cc_start: 0.8964 (mtp) cc_final: 0.8531 (mtm) REVERT: A 917 GLU cc_start: 0.8371 (tt0) cc_final: 0.7819 (tp30) REVERT: A 968 MET cc_start: 0.8308 (tpt) cc_final: 0.7891 (mmm) REVERT: A 989 ASN cc_start: 0.8208 (m-40) cc_final: 0.7820 (m-40) outliers start: 22 outliers final: 8 residues processed: 147 average time/residue: 0.6472 time to fit residues: 100.1610 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 43 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 643 GLN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.135491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106594 restraints weight = 8867.374| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.59 r_work: 0.2981 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7986 Z= 0.111 Angle : 0.488 5.671 10846 Z= 0.252 Chirality : 0.041 0.127 1273 Planarity : 0.004 0.037 1377 Dihedral : 6.553 139.679 1079 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.43 % Allowed : 14.12 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1007 helix: 0.54 (0.23), residues: 510 sheet: -0.89 (0.46), residues: 119 loop : -0.67 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.012 0.001 TYR A 842 PHE 0.013 0.001 PHE A 367 TRP 0.009 0.001 TRP A1016 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7985) covalent geometry : angle 0.48747 / 0.25 (10844) SS BOND : bond 0.00560 / 0.29 ( 1) SS BOND : angle 0.78589 / 0.44 ( 2) hydrogen bonds : bond 0.03973 / 2.60 ( 399) hydrogen bonds : angle 4.21759 / 2.97 ( 1257) *********************** 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 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.301 Fit side-chains REVERT: A 20 GLU cc_start: 0.7927 (pt0) cc_final: 0.7697 (pt0) REVERT: A 27 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: A 77 TRP cc_start: 0.7978 (t60) cc_final: 0.7758 (t-100) REVERT: A 135 LYS cc_start: 0.7771 (pttt) cc_final: 0.7251 (mmtp) REVERT: A 239 MET cc_start: 0.5291 (mtt) cc_final: 0.3917 (tpt) REVERT: A 370 ASP cc_start: 0.6581 (t0) cc_final: 0.6356 (t0) REVERT: A 371 ARG cc_start: 0.6730 (ptp-110) cc_final: 0.6023 (ptp90) REVERT: A 397 LYS cc_start: 0.7885 (tptp) cc_final: 0.7488 (tmtt) REVERT: A 431 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8425 (mttp) REVERT: A 510 LYS cc_start: 0.8297 (mttt) cc_final: 0.8021 (mtpp) REVERT: A 528 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8484 (tpp-160) REVERT: A 541 LYS cc_start: 0.8610 (tttt) cc_final: 0.8231 (ttmt) REVERT: A 549 ARG cc_start: 0.7687 (mtt180) cc_final: 0.6894 (ttp-110) REVERT: A 568 ASN cc_start: 0.7915 (m110) cc_final: 0.7580 (m-40) REVERT: A 585 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7675 (mttt) REVERT: A 719 MET cc_start: 0.9140 (mmm) cc_final: 0.8557 (mmt) REVERT: A 797 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8144 (p) REVERT: A 896 MET cc_start: 0.8962 (mtp) cc_final: 0.8525 (mtm) REVERT: A 917 GLU cc_start: 0.8465 (tt0) cc_final: 0.7908 (tp30) REVERT: A 989 ASN cc_start: 0.8203 (m-40) cc_final: 0.7927 (m-40) outliers start: 21 outliers final: 8 residues processed: 138 average time/residue: 0.6461 time to fit residues: 93.9562 Evaluate side-chains 122 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 398 ASP Chi-restraints excluded: chain A residue 540 VAL 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 46 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3466 r_free = 0.3466 target = 0.132495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103749 restraints weight = 9012.593| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.56 r_work: 0.3014 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7986 Z= 0.172 Angle : 0.551 6.016 10846 Z= 0.281 Chirality : 0.044 0.138 1273 Planarity : 0.004 0.038 1377 Dihedral : 7.028 152.136 1079 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.24 % Allowed : 14.12 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.26), residues: 1007 helix: 0.86 (0.23), residues: 509 sheet: -0.81 (0.46), residues: 119 loop : -0.53 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 491 TYR 0.016 0.002 TYR A 842 PHE 0.016 0.001 PHE A 367 TRP 0.010 0.001 TRP A1016 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 ( 7985) covalent geometry : angle 0.55064 / 0.28 (10844) SS BOND : bond 0.00930 / 0.49 ( 1) SS BOND : angle 1.13219 / 0.63 ( 2) hydrogen bonds : bond 0.04572 / 3.00 ( 399) hydrogen bonds : angle 4.30975 / 3.04 ( 1257) *********************** 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 139 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.373 Fit side-chains REVERT: A 20 GLU cc_start: 0.7951 (pt0) cc_final: 0.7696 (pt0) REVERT: A 27 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7191 (tp30) REVERT: A 77 TRP cc_start: 0.7998 (t60) cc_final: 0.7659 (t-100) REVERT: A 135 LYS cc_start: 0.7896 (pttt) cc_final: 0.7294 (mmtp) REVERT: A 143 LYS cc_start: 0.8551 (pttt) cc_final: 0.8166 (ptmt) REVERT: A 239 MET cc_start: 0.5297 (mtt) cc_final: 0.4080 (tpt) REVERT: A 370 ASP cc_start: 0.6800 (t0) cc_final: 0.6534 (t0) REVERT: A 371 ARG cc_start: 0.6497 (ptp-110) cc_final: 0.5804 (ptp90) REVERT: A 397 LYS cc_start: 0.7953 (tptp) cc_final: 0.7548 (tmtt) REVERT: A 431 LYS cc_start: 0.8788 (ttmm) cc_final: 0.8478 (mttp) REVERT: A 510 LYS cc_start: 0.8322 (mttt) cc_final: 0.8081 (mtpp) REVERT: A 528 ARG cc_start: 0.8768 (tpp-160) cc_final: 0.8503 (tpp-160) REVERT: A 529 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8201 (m) REVERT: A 541 LYS cc_start: 0.8653 (tttt) cc_final: 0.8409 (ttmt) REVERT: A 549 ARG cc_start: 0.7660 (mtt180) cc_final: 0.6979 (ttp-110) REVERT: A 585 LYS cc_start: 0.8412 (mtpp) cc_final: 0.7840 (mttt) REVERT: A 604 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8129 (mm) REVERT: A 719 MET cc_start: 0.9221 (mmm) cc_final: 0.8690 (mmt) REVERT: A 797 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8374 (p) REVERT: A 896 MET cc_start: 0.8965 (mtp) cc_final: 0.8587 (mtm) REVERT: A 989 ASN cc_start: 0.8114 (m-40) cc_final: 0.7882 (m-40) outliers start: 28 outliers final: 14 residues processed: 128 average time/residue: 0.6795 time to fit residues: 91.5926 Evaluate side-chains 128 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 529 VAL 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 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 19 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3489 r_free = 0.3489 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105882 restraints weight = 8977.449| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.55 r_work: 0.3022 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7986 Z= 0.129 Angle : 0.510 5.710 10846 Z= 0.261 Chirality : 0.042 0.130 1273 Planarity : 0.004 0.034 1377 Dihedral : 7.015 154.166 1079 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.24 % Allowed : 14.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.26), residues: 1007 helix: 1.14 (0.24), residues: 509 sheet: -0.72 (0.46), residues: 119 loop : -0.38 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 923 TYR 0.013 0.001 TYR A 295 PHE 0.015 0.001 PHE A 367 TRP 0.009 0.001 TRP A1016 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7985) covalent geometry : angle 0.51000 / 0.26 (10844) SS BOND : bond 0.00691 / 0.36 ( 1) SS BOND : angle 0.96368 / 0.54 ( 2) hydrogen bonds : bond 0.03987 / 2.62 ( 399) hydrogen bonds : angle 4.13555 / 2.92 ( 1257) *********************** 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 142 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.296 Fit side-chains REVERT: A 20 GLU cc_start: 0.7949 (pt0) cc_final: 0.7691 (pt0) REVERT: A 27 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: A 65 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 77 TRP cc_start: 0.7984 (t60) cc_final: 0.7643 (t-100) REVERT: A 135 LYS cc_start: 0.7894 (pttt) cc_final: 0.7357 (mmtp) REVERT: A 143 LYS cc_start: 0.8550 (pttt) cc_final: 0.8164 (ptmt) REVERT: A 174 ARG cc_start: 0.8345 (mtt-85) cc_final: 0.8001 (mtp180) REVERT: A 239 MET cc_start: 0.5201 (mtt) cc_final: 0.4021 (tpt) REVERT: A 370 ASP cc_start: 0.6745 (t0) cc_final: 0.6534 (t0) REVERT: A 371 ARG cc_start: 0.6417 (ptp-110) cc_final: 0.5693 (ptp90) REVERT: A 397 LYS cc_start: 0.7957 (tptp) cc_final: 0.7506 (tmtt) REVERT: A 406 GLN cc_start: 0.7056 (mp10) cc_final: 0.6839 (mp10) REVERT: A 431 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8500 (mttp) REVERT: A 467 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7886 (mtt90) REVERT: A 510 LYS cc_start: 0.8312 (mttt) cc_final: 0.8082 (mtpp) REVERT: A 528 ARG cc_start: 0.8761 (tpp-160) cc_final: 0.8193 (tpp-160) REVERT: A 529 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8177 (m) REVERT: A 541 LYS cc_start: 0.8638 (tttt) cc_final: 0.8388 (ttmt) REVERT: A 549 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7056 (mtp180) REVERT: A 568 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (m-40) REVERT: A 585 LYS cc_start: 0.8409 (mtpp) cc_final: 0.7775 (mttt) REVERT: A 719 MET cc_start: 0.9195 (mmm) cc_final: 0.8681 (mmp) REVERT: A 797 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8239 (p) REVERT: A 891 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8206 (mp0) REVERT: A 896 MET cc_start: 0.8949 (mtp) cc_final: 0.8631 (mtm) REVERT: A 989 ASN cc_start: 0.8096 (m-40) cc_final: 0.7759 (m-40) outliers start: 28 outliers final: 13 residues processed: 135 average time/residue: 0.6519 time to fit residues: 92.8535 Evaluate side-chains 127 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 398 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3462 r_free = 0.3462 target = 0.132253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103527 restraints weight = 8981.143| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.56 r_work: 0.3008 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7986 Z= 0.163 Angle : 0.548 5.895 10846 Z= 0.280 Chirality : 0.043 0.136 1273 Planarity : 0.004 0.035 1377 Dihedral : 7.202 160.881 1079 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.59 % Allowed : 15.05 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.26), residues: 1007 helix: 1.12 (0.24), residues: 509 sheet: -0.50 (0.45), residues: 129 loop : -0.39 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 923 TYR 0.015 0.002 TYR A 842 PHE 0.015 0.001 PHE A 367 TRP 0.009 0.001 TRP A1016 HIS 0.003 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 7985) covalent geometry : angle 0.54837 / 0.28 (10844) SS BOND : bond 0.01031 / 0.54 ( 1) SS BOND : angle 0.36829 / 0.22 ( 2) hydrogen bonds : bond 0.04397 / 2.88 ( 399) hydrogen bonds : angle 4.21569 / 2.98 ( 1257) *********************** 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 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.303 Fit side-chains REVERT: A 20 GLU cc_start: 0.7978 (pt0) cc_final: 0.7704 (pt0) REVERT: A 27 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7213 (tp30) REVERT: A 65 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8194 (mp) REVERT: A 77 TRP cc_start: 0.8020 (t60) cc_final: 0.7698 (t-100) REVERT: A 135 LYS cc_start: 0.7922 (pttt) cc_final: 0.7348 (mmtp) REVERT: A 143 LYS cc_start: 0.8561 (pttt) cc_final: 0.8166 (ptmt) REVERT: A 239 MET cc_start: 0.5261 (mtt) cc_final: 0.4057 (tpt) REVERT: A 361 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: A 370 ASP cc_start: 0.6715 (t0) cc_final: 0.6489 (t0) REVERT: A 371 ARG cc_start: 0.6496 (ptp-110) cc_final: 0.5821 (ptp90) REVERT: A 397 LYS cc_start: 0.7973 (tptp) cc_final: 0.7513 (tmtt) REVERT: A 406 GLN cc_start: 0.7073 (mp10) cc_final: 0.6831 (mp10) REVERT: A 431 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8477 (mttp) REVERT: A 462 LEU cc_start: 0.8069 (mt) cc_final: 0.7848 (mt) REVERT: A 506 THR cc_start: 0.3123 (OUTLIER) cc_final: 0.2845 (t) REVERT: A 510 LYS cc_start: 0.8312 (mttt) cc_final: 0.8079 (mtpp) REVERT: A 528 ARG cc_start: 0.8766 (tpp-160) cc_final: 0.8217 (tpp-160) REVERT: A 529 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8178 (m) REVERT: A 541 LYS cc_start: 0.8638 (tttt) cc_final: 0.8346 (ttmt) REVERT: A 549 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7127 (mtp180) REVERT: A 585 LYS cc_start: 0.8489 (mtpp) cc_final: 0.7821 (mttt) REVERT: A 604 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8162 (mm) REVERT: A 719 MET cc_start: 0.9232 (mmm) cc_final: 0.8759 (mmt) REVERT: A 797 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8360 (p) REVERT: A 891 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: A 896 MET cc_start: 0.8917 (mtp) cc_final: 0.8594 (mtm) REVERT: A 989 ASN cc_start: 0.8123 (m-40) cc_final: 0.7870 (m-40) outliers start: 31 outliers final: 17 residues processed: 131 average time/residue: 0.6710 time to fit residues: 92.4119 Evaluate side-chains 133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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 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 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 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 5 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3461 r_free = 0.3461 target = 0.132162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103539 restraints weight = 9018.905| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.55 r_work: 0.3008 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7986 Z= 0.165 Angle : 0.548 5.912 10846 Z= 0.279 Chirality : 0.044 0.135 1273 Planarity : 0.004 0.035 1377 Dihedral : 7.340 165.415 1079 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.59 % Allowed : 15.16 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.27), residues: 1007 helix: 1.16 (0.24), residues: 509 sheet: -0.60 (0.46), residues: 124 loop : -0.30 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 923 TYR 0.015 0.002 TYR A 842 PHE 0.015 0.001 PHE A 367 TRP 0.009 0.001 TRP A1016 HIS 0.004 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.16 ( 7985) covalent geometry : angle 0.54807 / 0.28 (10844) SS BOND : bond 0.00907 / 0.48 ( 1) SS BOND : angle 0.51607 / 0.30 ( 2) hydrogen bonds : bond 0.04370 / 2.86 ( 399) hydrogen bonds : angle 4.21745 / 2.98 ( 1257) *********************** 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 143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.296 Fit side-chains REVERT: A 20 GLU cc_start: 0.7994 (pt0) cc_final: 0.7768 (pt0) REVERT: A 27 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: A 31 LYS cc_start: 0.8340 (mtmm) cc_final: 0.7420 (mmtp) REVERT: A 65 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8199 (mp) REVERT: A 77 TRP cc_start: 0.8152 (t60) cc_final: 0.7686 (t-100) REVERT: A 135 LYS cc_start: 0.7946 (pttt) cc_final: 0.7347 (mmtp) REVERT: A 143 LYS cc_start: 0.8571 (pttt) cc_final: 0.8173 (ptmt) REVERT: A 239 MET cc_start: 0.5201 (mtt) cc_final: 0.4002 (tpt) REVERT: A 361 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8340 (mtm) REVERT: A 370 ASP cc_start: 0.6710 (t0) cc_final: 0.6491 (t0) REVERT: A 371 ARG cc_start: 0.6489 (ptp-110) cc_final: 0.5917 (ptp90) REVERT: A 397 LYS cc_start: 0.7999 (tptp) cc_final: 0.7516 (tmtt) REVERT: A 431 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8472 (mttp) REVERT: A 462 LEU cc_start: 0.8094 (mt) cc_final: 0.7826 (mt) REVERT: A 506 THR cc_start: 0.3122 (OUTLIER) cc_final: 0.2844 (t) REVERT: A 510 LYS cc_start: 0.8335 (mttt) cc_final: 0.8088 (mttm) REVERT: A 528 ARG cc_start: 0.8764 (tpp-160) cc_final: 0.8231 (tpp-160) REVERT: A 541 LYS cc_start: 0.8614 (tttt) cc_final: 0.8279 (ttmt) REVERT: A 549 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7135 (mtp180) REVERT: A 585 LYS cc_start: 0.8463 (mtpp) cc_final: 0.7784 (mttt) REVERT: A 604 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8176 (mm) REVERT: A 719 MET cc_start: 0.9238 (mmm) cc_final: 0.8803 (mmt) REVERT: A 797 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8393 (p) REVERT: A 891 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: A 896 MET cc_start: 0.8915 (mtp) cc_final: 0.8608 (mtm) REVERT: A 989 ASN cc_start: 0.8138 (m-40) cc_final: 0.7895 (m-40) outliers start: 31 outliers final: 18 residues processed: 134 average time/residue: 0.6694 time to fit residues: 94.2866 Evaluate side-chains 136 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 604 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.136887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109143 restraints weight = 9000.348| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.52 r_work: 0.2999 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7986 Z= 0.103 Angle : 0.495 5.927 10846 Z= 0.252 Chirality : 0.041 0.125 1273 Planarity : 0.004 0.032 1377 Dihedral : 7.001 160.228 1079 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.01 % Allowed : 16.32 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.27), residues: 1007 helix: 1.45 (0.24), residues: 510 sheet: -0.28 (0.45), residues: 134 loop : -0.23 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 923 TYR 0.012 0.001 TYR A 295 PHE 0.015 0.001 PHE A 367 TRP 0.011 0.001 TRP A 793 HIS 0.001 0.000 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 7985) covalent geometry : angle 0.49537 / 0.25 (10844) SS BOND : bond 0.00490 / 0.26 ( 1) SS BOND : angle 0.37838 / 0.22 ( 2) hydrogen bonds : bond 0.03474 / 2.28 ( 399) hydrogen bonds : angle 3.96820 / 2.80 ( 1257) *********************** 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 146 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.311 Fit side-chains REVERT: A 20 GLU cc_start: 0.7911 (pt0) cc_final: 0.7656 (pt0) REVERT: A 31 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7468 (mmtp) REVERT: A 77 TRP cc_start: 0.8222 (t60) cc_final: 0.7738 (t-100) REVERT: A 135 LYS cc_start: 0.7917 (pttt) cc_final: 0.7413 (mmtp) REVERT: A 239 MET cc_start: 0.5182 (mtt) cc_final: 0.3894 (tpt) REVERT: A 371 ARG cc_start: 0.6301 (ptp-110) cc_final: 0.5699 (ptp90) REVERT: A 397 LYS cc_start: 0.7997 (tptp) cc_final: 0.7485 (tmtt) REVERT: A 431 LYS cc_start: 0.8748 (ttmm) cc_final: 0.8507 (mttp) REVERT: A 462 LEU cc_start: 0.8135 (mt) cc_final: 0.7849 (mt) REVERT: A 467 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7539 (mmt90) REVERT: A 506 THR cc_start: 0.2962 (OUTLIER) cc_final: 0.2729 (t) REVERT: A 510 LYS cc_start: 0.8311 (mttt) cc_final: 0.8076 (mttm) REVERT: A 528 ARG cc_start: 0.8653 (tpp-160) cc_final: 0.8134 (tpp-160) REVERT: A 541 LYS cc_start: 0.8552 (tttt) cc_final: 0.8259 (ttmt) REVERT: A 549 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7040 (mtp180) REVERT: A 585 LYS cc_start: 0.8458 (mtpp) cc_final: 0.7790 (mttt) REVERT: A 604 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 719 MET cc_start: 0.9142 (mmm) cc_final: 0.8688 (mmt) REVERT: A 797 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 896 MET cc_start: 0.8909 (mtp) cc_final: 0.8612 (mtm) outliers start: 26 outliers final: 11 residues processed: 136 average time/residue: 0.5947 time to fit residues: 85.5441 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 467 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 88 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.108741 restraints weight = 8884.443| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.51 r_work: 0.3100 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7986 Z= 0.108 Angle : 0.512 9.125 10846 Z= 0.256 Chirality : 0.041 0.126 1273 Planarity : 0.004 0.032 1377 Dihedral : 6.940 157.786 1079 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.55 % Allowed : 17.25 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 1007 helix: 1.50 (0.24), residues: 514 sheet: -0.27 (0.45), residues: 134 loop : -0.16 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 923 TYR 0.012 0.001 TYR A 842 PHE 0.014 0.001 PHE A 367 TRP 0.009 0.001 TRP A 854 HIS 0.001 0.000 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 7985) covalent geometry : angle 0.51230 / 0.26 (10844) SS BOND : bond 0.00566 / 0.30 ( 1) SS BOND : angle 0.41224 / 0.24 ( 2) hydrogen bonds : bond 0.03588 / 2.35 ( 399) hydrogen bonds : angle 3.96516 / 2.80 ( 1257) *********************** 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 131 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.307 Fit side-chains REVERT: A 20 GLU cc_start: 0.7897 (pt0) cc_final: 0.7657 (pt0) REVERT: A 31 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7449 (mmtp) REVERT: A 65 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 77 TRP cc_start: 0.8223 (t60) cc_final: 0.7791 (t-100) REVERT: A 135 LYS cc_start: 0.7869 (pttt) cc_final: 0.7438 (mmtp) REVERT: A 174 ARG cc_start: 0.8427 (mtt-85) cc_final: 0.7965 (mtp180) REVERT: A 239 MET cc_start: 0.5197 (mtt) cc_final: 0.3906 (tpt) REVERT: A 371 ARG cc_start: 0.6448 (ptp-110) cc_final: 0.5977 (ptp90) REVERT: A 397 LYS cc_start: 0.8006 (tptp) cc_final: 0.7546 (tmtt) REVERT: A 431 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8537 (mttp) REVERT: A 462 LEU cc_start: 0.8124 (mt) cc_final: 0.7828 (mt) REVERT: A 510 LYS cc_start: 0.8342 (mttt) cc_final: 0.8113 (mttm) REVERT: A 528 ARG cc_start: 0.8717 (tpp-160) cc_final: 0.8515 (tpp-160) REVERT: A 541 LYS cc_start: 0.8544 (tttt) cc_final: 0.8301 (ttmt) REVERT: A 549 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7077 (mtm110) REVERT: A 585 LYS cc_start: 0.8551 (mtpp) cc_final: 0.7819 (mttt) REVERT: A 604 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8068 (mm) REVERT: A 719 MET cc_start: 0.9162 (mmm) cc_final: 0.8672 (mmt) REVERT: A 797 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 891 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: A 896 MET cc_start: 0.8911 (mtp) cc_final: 0.8631 (mtm) outliers start: 22 outliers final: 12 residues processed: 127 average time/residue: 0.6701 time to fit residues: 89.5394 Evaluate side-chains 124 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 307 ILE 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 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 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 77 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.0470 chunk 29 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 874 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109089 restraints weight = 8800.374| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.49 r_work: 0.3052 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7986 Z= 0.110 Angle : 0.520 9.397 10846 Z= 0.259 Chirality : 0.041 0.126 1273 Planarity : 0.004 0.033 1377 Dihedral : 6.907 156.556 1079 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.97 % Allowed : 17.82 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.27), residues: 1007 helix: 1.53 (0.24), residues: 514 sheet: -0.26 (0.45), residues: 134 loop : -0.11 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 923 TYR 0.012 0.001 TYR A 842 PHE 0.014 0.001 PHE A 367 TRP 0.009 0.001 TRP A 854 HIS 0.001 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7985) covalent geometry : angle 0.52051 / 0.26 (10844) SS BOND : bond 0.00574 / 0.30 ( 1) SS BOND : angle 0.37821 / 0.22 ( 2) hydrogen bonds : bond 0.03553 / 2.33 ( 399) hydrogen bonds : angle 3.95698 / 2.80 ( 1257) ********************** 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 126 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.299 Fit side-chains REVERT: A 20 GLU cc_start: 0.7920 (pt0) cc_final: 0.7686 (pt0) REVERT: A 31 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7485 (mmtp) REVERT: A 65 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 77 TRP cc_start: 0.8208 (t60) cc_final: 0.7748 (t-100) REVERT: A 135 LYS cc_start: 0.7864 (pttt) cc_final: 0.7465 (mmtp) REVERT: A 174 ARG cc_start: 0.8437 (mtt-85) cc_final: 0.7977 (mtp180) REVERT: A 239 MET cc_start: 0.5184 (mtt) cc_final: 0.4481 (ttp) REVERT: A 371 ARG cc_start: 0.6440 (ptp-110) cc_final: 0.6000 (ptp90) REVERT: A 397 LYS cc_start: 0.8026 (tptp) cc_final: 0.7706 (tmtt) REVERT: A 431 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8549 (mttp) REVERT: A 462 LEU cc_start: 0.8129 (mt) cc_final: 0.7875 (mt) REVERT: A 510 LYS cc_start: 0.8394 (mttt) cc_final: 0.8167 (mttm) REVERT: A 528 ARG cc_start: 0.8831 (tpp-160) cc_final: 0.8289 (tpp-160) REVERT: A 541 LYS cc_start: 0.8582 (tttt) cc_final: 0.8247 (ttmt) REVERT: A 549 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7142 (mtm110) REVERT: A 585 LYS cc_start: 0.8484 (mtpp) cc_final: 0.7840 (mttt) REVERT: A 604 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8056 (mm) REVERT: A 719 MET cc_start: 0.9180 (mmm) cc_final: 0.8689 (mmt) REVERT: A 797 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8255 (p) REVERT: A 896 MET cc_start: 0.8934 (mtp) cc_final: 0.8647 (mtm) outliers start: 17 outliers final: 12 residues processed: 123 average time/residue: 0.6405 time to fit residues: 83.1345 Evaluate side-chains 123 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 307 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 ASN A 822 ASN A 874 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107176 restraints weight = 8844.845| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.49 r_work: 0.2957 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7986 Z= 0.152 Angle : 0.561 9.307 10846 Z= 0.281 Chirality : 0.043 0.134 1273 Planarity : 0.004 0.035 1377 Dihedral : 7.166 161.171 1079 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.43 % Allowed : 17.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.27), residues: 1007 helix: 1.34 (0.23), residues: 515 sheet: -0.31 (0.45), residues: 134 loop : -0.17 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 923 TYR 0.015 0.002 TYR A 842 PHE 0.014 0.001 PHE A 367 TRP 0.010 0.001 TRP A1016 HIS 0.002 0.001 HIS A 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 7985) covalent geometry : angle 0.56096 / 0.28 (10844) SS BOND : bond 0.00786 / 0.41 ( 1) SS BOND : angle 0.53094 / 0.31 ( 2) hydrogen bonds : bond 0.04156 / 2.72 ( 399) hydrogen bonds : angle 4.13390 / 2.93 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.42 seconds wall clock time: 54 minutes 4.69 seconds (3244.69 seconds total)