Starting phenix.real_space_refine on Wed Feb 12 09:44:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ln8_0927/02_2025/6ln8_0927.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ln8_0927/02_2025/6ln8_0927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ln8_0927/02_2025/6ln8_0927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ln8_0927/02_2025/6ln8_0927.map" model { file = "/net/cci-nas-00/data/ceres_data/6ln8_0927/02_2025/6ln8_0927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ln8_0927/02_2025/6ln8_0927.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Mg 1 5.21 5 S 57 5.16 5 Be 1 3.05 5 C 4932 2.51 5 N 1294 2.21 5 O 1451 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7739 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7734 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 957} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.72, per 1000 atoms: 0.61 Number of scatterers: 7739 At special positions: 0 Unit cell: (88.395, 92.13, 145.665, 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) S 57 16.00 Mg 1 11.99 F 3 9.00 O 1451 8.00 N 1294 7.00 C 4932 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 979.8 milliseconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 54.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.713A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.677A pdb=" N GLU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 84 through 118 removed outlier: 5.083A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.638A pdb=" N ALA A 118 " --> pdb=" O ASN A 114 " (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 229 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 247 through 276 Processing helix chain 'A' and resid 290 through 306 removed outlier: 4.320A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 328 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.632A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.929A pdb=" N ASN A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 4.468A pdb=" N LEU A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 516 through 522 Processing helix chain 'A' and resid 537 through 552 Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.090A pdb=" N LYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 removed outlier: 3.735A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 661 through 672 Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.739A 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 711 Processing helix chain 'A' and resid 723 through 730 Processing helix chain 'A' and resid 739 through 781 removed outlier: 3.872A pdb=" N VAL A 743 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 754 " --> pdb=" O ARG A 750 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 806 removed outlier: 3.938A pdb=" N TRP A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 814 through 818 removed outlier: 4.042A pdb=" N LYS A 818 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 857 removed outlier: 3.844A pdb=" N ILE A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 873 through 877 removed outlier: 3.601A pdb=" N LYS A 876 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.471A pdb=" N MET A 896 " --> pdb=" O SER A 892 " (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 956 removed outlier: 3.599A pdb=" N ILE A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 974 Processing helix chain 'A' and resid 974 through 990 removed outlier: 3.981A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1030 Proline residue: A1024 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141 removed outlier: 12.144A pdb=" N MET A 126 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N ALA A 154 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS A 218 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE A 168 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET A 220 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 4.479A pdb=" N LEU A 173 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ARG A 174 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 213 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.205A pdb=" N GLY A 716 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU A 734 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA A 718 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 697 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE A 717 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET A 699 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N MET A 719 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLY A 701 " --> pdb=" O MET A 719 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N PHE A 675 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET A 622 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 19.639A pdb=" N CYS A 524 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 17.183A pdb=" N PHE A 367 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 14.582A pdb=" N HIS A 526 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N LEU A 369 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG A 528 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 7.884A 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: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.642A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.736A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS A 524 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 592 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N HIS A 526 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY A 594 " --> pdb=" O HIS A 526 " (cutoff:3.500A) removed outlier: 9.403A pdb=" N ARG A 528 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 12.816A pdb=" N VAL A 596 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 396 removed outlier: 6.768A pdb=" N SER A 378 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL A 363 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 599 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 369 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N VAL A 593 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 14.642A pdb=" N ARG A 371 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 15.736A pdb=" N THR A 591 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 493 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A 487 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 495 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 428 439 hydrogen bonds defined for protein. 1269 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: 2.79 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2532 1.34 - 1.46: 1398 1.46 - 1.58: 3862 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7880 Sorted by residual: bond pdb=" F2 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" F3 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 8.06e+00 bond pdb=" C ASP A 398 " pdb=" O ASP A 398 " ideal model delta sigma weight residual 1.234 1.247 -0.013 1.30e-02 5.92e+03 9.31e-01 bond pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.55e-02 4.16e+03 6.89e-01 ... (remaining 7875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 10644 2.78 - 5.56: 46 5.56 - 8.34: 1 8.34 - 11.12: 1 11.12 - 13.90: 1 Bond angle restraints: 10693 Sorted by residual: angle pdb=" F2 BEF A2001 " pdb="BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 119.96 106.06 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 120.12 109.98 10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N ASP A 398 " pdb=" CA ASP A 398 " pdb=" C ASP A 398 " ideal model delta sigma weight residual 112.13 107.72 4.41 1.37e+00 5.33e-01 1.04e+01 angle pdb=" N THR A 358 " pdb=" CA THR A 358 " pdb=" C THR A 358 " ideal model delta sigma weight residual 110.53 106.96 3.57 1.29e+00 6.01e-01 7.65e+00 angle pdb=" F1 BEF A2001 " pdb="BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 119.91 112.30 7.61 3.00e+00 1.11e-01 6.44e+00 ... (remaining 10688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4279 16.00 - 32.01: 397 32.01 - 48.01: 89 48.01 - 64.01: 7 64.01 - 80.01: 5 Dihedral angle restraints: 4777 sinusoidal: 1882 harmonic: 2895 Sorted by residual: dihedral pdb=" CA LEU A 947 " pdb=" C LEU A 947 " pdb=" N TYR A 948 " pdb=" CA TYR A 948 " ideal model delta harmonic sigma weight residual -180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA THR A 357 " pdb=" C THR A 357 " pdb=" N THR A 358 " pdb=" CA THR A 358 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.98e+00 dihedral pdb=" CB MET A 908 " pdb=" CG MET A 908 " pdb=" SD MET A 908 " pdb=" CE MET A 908 " ideal model delta sinusoidal sigma weight residual 60.00 112.21 -52.21 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 4774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 735 0.027 - 0.055: 345 0.055 - 0.082: 102 0.082 - 0.110: 60 0.110 - 0.137: 17 Chirality restraints: 1259 Sorted by residual: chirality pdb=" CA ILE A 307 " pdb=" N ILE A 307 " pdb=" C ILE A 307 " pdb=" CB ILE A 307 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 621 " pdb=" N ILE A 621 " pdb=" C ILE A 621 " pdb=" CB ILE A 621 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 150 " pdb=" N ILE A 150 " pdb=" C ILE A 150 " pdb=" CB ILE A 150 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1256 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 975 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" C LEU A 796 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 952 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 953 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 953 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 953 " 0.021 5.00e-02 4.00e+02 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 61 2.62 - 3.19: 7035 3.19 - 3.76: 12017 3.76 - 4.33: 16964 4.33 - 4.90: 28144 Nonbonded interactions: 64221 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.051 2.170 nonbonded pdb=" F1 BEF A2001 " pdb="MG MG A2002 " model vdw 2.059 2.120 nonbonded pdb=" OD2 ASP A 351 " pdb=" F1 BEF A2001 " model vdw 2.085 2.990 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.097 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.101 2.170 ... (remaining 64216 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: 0.210 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.003 0.084 7880 Z= 0.209 Angle : 0.562 13.901 10693 Z= 0.320 Chirality : 0.039 0.137 1259 Planarity : 0.004 0.041 1362 Dihedral : 12.814 80.014 2901 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.22), residues: 997 helix: -1.61 (0.20), residues: 506 sheet: -1.80 (0.43), residues: 105 loop : -1.82 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 PHE 0.016 0.001 PHE A 759 TYR 0.015 0.001 TYR A 836 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.883 Fit side-chains REVERT: A 63 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7612 (mtm-85) REVERT: A 128 LYS cc_start: 0.8284 (mttt) cc_final: 0.8037 (mtmm) REVERT: A 140 ILE cc_start: 0.8162 (pt) cc_final: 0.7732 (pt) REVERT: A 545 MET cc_start: 0.7955 (mmm) cc_final: 0.7627 (tpp) REVERT: A 586 TYR cc_start: 0.6963 (m-10) cc_final: 0.6597 (m-80) REVERT: A 732 MET cc_start: 0.8480 (ttm) cc_final: 0.8260 (ttt) REVERT: A 816 MET cc_start: 0.7378 (mmm) cc_final: 0.6963 (mmm) REVERT: A 1028 TRP cc_start: 0.7329 (t60) cc_final: 0.6918 (t60) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2717 time to fit residues: 50.1274 Evaluate side-chains 113 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 177 GLN A 428 ASN A 582 ASN A 615 GLN A 671 ASN A 682 HIS A 868 GLN A 943 HIS A 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.172891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131154 restraints weight = 8298.003| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.80 r_work: 0.3251 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7880 Z= 0.296 Angle : 0.550 5.511 10693 Z= 0.289 Chirality : 0.043 0.152 1259 Planarity : 0.005 0.042 1362 Dihedral : 4.072 16.866 1061 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.17 % Allowed : 11.24 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 997 helix: -0.30 (0.22), residues: 518 sheet: -1.64 (0.42), residues: 105 loop : -1.13 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 831 HIS 0.003 0.001 HIS A 15 PHE 0.024 0.002 PHE A 759 TYR 0.016 0.002 TYR A 762 ARG 0.006 0.001 ARG A 666 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.863 Fit side-chains REVERT: A 63 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7543 (mtm-85) REVERT: A 140 ILE cc_start: 0.8160 (pt) cc_final: 0.7740 (pt) REVERT: A 143 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7863 (mtmm) REVERT: A 297 LYS cc_start: 0.6837 (mtpp) cc_final: 0.6552 (mttp) REVERT: A 518 GLU cc_start: 0.8347 (pp20) cc_final: 0.7786 (pp20) REVERT: A 536 MET cc_start: 0.7432 (ttm) cc_final: 0.6906 (ttm) REVERT: A 586 TYR cc_start: 0.7058 (m-10) cc_final: 0.6682 (m-80) REVERT: A 816 MET cc_start: 0.8144 (mmm) cc_final: 0.7742 (mmm) REVERT: A 1028 TRP cc_start: 0.7593 (t60) cc_final: 0.6969 (t60) outliers start: 10 outliers final: 9 residues processed: 125 average time/residue: 0.2490 time to fit residues: 40.8769 Evaluate side-chains 116 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 428 ASN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133644 restraints weight = 8332.468| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.80 r_work: 0.3304 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7880 Z= 0.147 Angle : 0.470 6.133 10693 Z= 0.246 Chirality : 0.040 0.139 1259 Planarity : 0.004 0.048 1362 Dihedral : 3.819 17.230 1061 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.64 % Allowed : 13.70 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 997 helix: 0.41 (0.23), residues: 520 sheet: -1.44 (0.43), residues: 103 loop : -0.81 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 927 HIS 0.002 0.000 HIS A 871 PHE 0.025 0.001 PHE A 759 TYR 0.014 0.001 TYR A 990 ARG 0.003 0.000 ARG A 655 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.902 Fit side-chains REVERT: A 120 LYS cc_start: 0.7374 (mttp) cc_final: 0.7004 (mmtp) REVERT: A 140 ILE cc_start: 0.8128 (pt) cc_final: 0.7708 (pt) REVERT: A 143 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7824 (mtmm) REVERT: A 297 LYS cc_start: 0.6852 (mtpp) cc_final: 0.6625 (mttp) REVERT: A 518 GLU cc_start: 0.8319 (pp20) cc_final: 0.7799 (pp20) REVERT: A 542 GLN cc_start: 0.7219 (pp30) cc_final: 0.6994 (pp30) REVERT: A 549 ARG cc_start: 0.7547 (mpp80) cc_final: 0.7245 (mtt90) REVERT: A 586 TYR cc_start: 0.7104 (m-10) cc_final: 0.6790 (m-80) REVERT: A 714 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: A 816 MET cc_start: 0.8078 (mmm) cc_final: 0.7723 (mmm) REVERT: A 1028 TRP cc_start: 0.7591 (t60) cc_final: 0.7005 (t60) outliers start: 14 outliers final: 7 residues processed: 127 average time/residue: 0.2429 time to fit residues: 40.6817 Evaluate side-chains 114 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 95 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.133179 restraints weight = 8318.127| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.80 r_work: 0.3301 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7880 Z= 0.165 Angle : 0.476 6.292 10693 Z= 0.246 Chirality : 0.040 0.144 1259 Planarity : 0.004 0.047 1362 Dihedral : 3.727 17.764 1061 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.22 % Allowed : 13.82 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 997 helix: 0.67 (0.23), residues: 520 sheet: -1.10 (0.44), residues: 102 loop : -0.63 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 PHE 0.025 0.001 PHE A 759 TYR 0.014 0.001 TYR A 990 ARG 0.003 0.000 ARG A 655 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.867 Fit side-chains REVERT: A 63 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7352 (mtm-85) REVERT: A 120 LYS cc_start: 0.7435 (mttp) cc_final: 0.7083 (mmtp) REVERT: A 140 ILE cc_start: 0.8150 (pt) cc_final: 0.7716 (pt) REVERT: A 143 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7838 (mtmm) REVERT: A 297 LYS cc_start: 0.6886 (mtpp) cc_final: 0.6619 (mttp) REVERT: A 518 GLU cc_start: 0.8321 (pp20) cc_final: 0.7809 (pp20) REVERT: A 549 ARG cc_start: 0.7650 (mpp80) cc_final: 0.7442 (mpp80) REVERT: A 583 PHE cc_start: 0.7081 (m-80) cc_final: 0.6656 (m-80) REVERT: A 714 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7905 (mm-30) REVERT: A 791 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7690 (mp) REVERT: A 816 MET cc_start: 0.8099 (mmm) cc_final: 0.7711 (mmm) REVERT: A 836 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.5664 (p90) REVERT: A 1028 TRP cc_start: 0.7631 (t60) cc_final: 0.7054 (t60) outliers start: 19 outliers final: 11 residues processed: 134 average time/residue: 0.2519 time to fit residues: 44.4966 Evaluate side-chains 121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 88 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135656 restraints weight = 8296.815| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.77 r_work: 0.3342 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7880 Z= 0.127 Angle : 0.460 6.366 10693 Z= 0.237 Chirality : 0.040 0.139 1259 Planarity : 0.004 0.045 1362 Dihedral : 3.634 17.258 1061 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.87 % Allowed : 15.46 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 997 helix: 0.99 (0.24), residues: 513 sheet: -1.00 (0.45), residues: 104 loop : -0.51 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 854 HIS 0.002 0.000 HIS A 871 PHE 0.025 0.001 PHE A 759 TYR 0.015 0.001 TYR A 990 ARG 0.006 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.719 Fit side-chains REVERT: A 120 LYS cc_start: 0.7498 (mttp) cc_final: 0.7109 (mmtp) REVERT: A 140 ILE cc_start: 0.8051 (pt) cc_final: 0.7653 (pt) REVERT: A 143 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7813 (mtmm) REVERT: A 266 LEU cc_start: 0.8093 (tt) cc_final: 0.7623 (tp) REVERT: A 297 LYS cc_start: 0.6712 (mtpp) cc_final: 0.6483 (mttp) REVERT: A 332 ILE cc_start: 0.8849 (mm) cc_final: 0.8554 (mt) REVERT: A 518 GLU cc_start: 0.8392 (pp20) cc_final: 0.7902 (pp20) REVERT: A 526 HIS cc_start: 0.7387 (m-70) cc_final: 0.7004 (m-70) REVERT: A 549 ARG cc_start: 0.7563 (mpp80) cc_final: 0.7141 (mpp80) REVERT: A 583 PHE cc_start: 0.7266 (m-80) cc_final: 0.6749 (m-80) REVERT: A 586 TYR cc_start: 0.7217 (m-80) cc_final: 0.6653 (m-80) REVERT: A 714 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: A 836 TYR cc_start: 0.6725 (OUTLIER) cc_final: 0.5549 (p90) REVERT: A 1028 TRP cc_start: 0.7635 (t60) cc_final: 0.7047 (t60) outliers start: 16 outliers final: 10 residues processed: 140 average time/residue: 0.2312 time to fit residues: 42.3329 Evaluate side-chains 134 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.177863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134864 restraints weight = 8298.192| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.81 r_work: 0.3314 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7880 Z= 0.165 Angle : 0.473 6.317 10693 Z= 0.244 Chirality : 0.041 0.145 1259 Planarity : 0.004 0.046 1362 Dihedral : 3.666 17.689 1061 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.22 % Allowed : 16.04 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.27), residues: 997 helix: 1.04 (0.24), residues: 513 sheet: -0.94 (0.46), residues: 104 loop : -0.43 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.002 0.000 HIS A 15 PHE 0.024 0.001 PHE A 759 TYR 0.014 0.001 TYR A 990 ARG 0.005 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7521 (mtm-85) REVERT: A 120 LYS cc_start: 0.7434 (mttp) cc_final: 0.7025 (mmtp) REVERT: A 140 ILE cc_start: 0.8120 (pt) cc_final: 0.7699 (pt) REVERT: A 143 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7842 (mtmm) REVERT: A 297 LYS cc_start: 0.6785 (mtpp) cc_final: 0.6517 (mttp) REVERT: A 332 ILE cc_start: 0.8918 (mm) cc_final: 0.8606 (mt) REVERT: A 518 GLU cc_start: 0.8401 (pp20) cc_final: 0.7930 (pp20) REVERT: A 526 HIS cc_start: 0.7403 (m-70) cc_final: 0.7035 (m-70) REVERT: A 583 PHE cc_start: 0.7399 (m-80) cc_final: 0.6913 (m-80) REVERT: A 586 TYR cc_start: 0.7281 (m-80) cc_final: 0.6747 (m-80) REVERT: A 714 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: A 836 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.5662 (p90) REVERT: A 1028 TRP cc_start: 0.7649 (t60) cc_final: 0.7047 (t60) outliers start: 19 outliers final: 13 residues processed: 138 average time/residue: 0.2417 time to fit residues: 43.4894 Evaluate side-chains 134 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 0.0370 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.0770 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.178186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.135777 restraints weight = 8296.504| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.80 r_work: 0.3326 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7880 Z= 0.143 Angle : 0.468 6.497 10693 Z= 0.240 Chirality : 0.040 0.143 1259 Planarity : 0.003 0.046 1362 Dihedral : 3.609 17.470 1061 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.69 % Allowed : 15.69 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 997 helix: 1.17 (0.24), residues: 512 sheet: -0.90 (0.47), residues: 104 loop : -0.37 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.001 0.000 HIS A 943 PHE 0.025 0.001 PHE A 759 TYR 0.015 0.001 TYR A 990 ARG 0.006 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7989 (mtt-85) cc_final: 0.7484 (mtm-85) REVERT: A 120 LYS cc_start: 0.7457 (mttp) cc_final: 0.7047 (mmtp) REVERT: A 140 ILE cc_start: 0.8110 (pt) cc_final: 0.7728 (pt) REVERT: A 143 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7834 (mtmm) REVERT: A 297 LYS cc_start: 0.6706 (mtpp) cc_final: 0.6439 (mttp) REVERT: A 332 ILE cc_start: 0.8903 (mm) cc_final: 0.8615 (mt) REVERT: A 518 GLU cc_start: 0.8389 (pp20) cc_final: 0.7908 (pp20) REVERT: A 526 HIS cc_start: 0.7393 (m-70) cc_final: 0.6993 (m-70) REVERT: A 536 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7214 (tpp) REVERT: A 583 PHE cc_start: 0.7435 (m-80) cc_final: 0.7000 (m-80) REVERT: A 586 TYR cc_start: 0.7310 (m-80) cc_final: 0.6906 (m-80) REVERT: A 714 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7808 (mm-30) REVERT: A 836 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.5620 (p90) REVERT: A 1028 TRP cc_start: 0.7601 (t60) cc_final: 0.7033 (t60) outliers start: 23 outliers final: 15 residues processed: 142 average time/residue: 0.2346 time to fit residues: 43.5415 Evaluate side-chains 137 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.173506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131688 restraints weight = 8397.325| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.93 r_work: 0.3242 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7880 Z= 0.308 Angle : 0.548 5.795 10693 Z= 0.283 Chirality : 0.044 0.160 1259 Planarity : 0.004 0.046 1362 Dihedral : 3.933 18.119 1061 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.69 % Allowed : 16.86 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 997 helix: 0.76 (0.23), residues: 514 sheet: -1.23 (0.45), residues: 107 loop : -0.44 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 793 HIS 0.003 0.001 HIS A 15 PHE 0.024 0.002 PHE A 759 TYR 0.016 0.002 TYR A 836 ARG 0.006 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7366 (mtm-85) REVERT: A 297 LYS cc_start: 0.6825 (mtpp) cc_final: 0.6561 (mttp) REVERT: A 480 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7740 (ttpp) REVERT: A 518 GLU cc_start: 0.8364 (pp20) cc_final: 0.7903 (pp20) REVERT: A 536 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7374 (ttm) REVERT: A 583 PHE cc_start: 0.7330 (m-80) cc_final: 0.6914 (m-80) REVERT: A 586 TYR cc_start: 0.7311 (m-80) cc_final: 0.6976 (m-80) REVERT: A 836 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.5657 (p90) REVERT: A 940 MET cc_start: 0.7924 (mmm) cc_final: 0.7684 (mmt) REVERT: A 1028 TRP cc_start: 0.7657 (t60) cc_final: 0.7082 (t60) outliers start: 23 outliers final: 18 residues processed: 136 average time/residue: 0.2274 time to fit residues: 40.3630 Evaluate side-chains 134 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.0050 chunk 82 optimal weight: 0.1980 chunk 72 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.177536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135801 restraints weight = 8442.013| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.81 r_work: 0.3317 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7880 Z= 0.141 Angle : 0.477 5.660 10693 Z= 0.247 Chirality : 0.040 0.149 1259 Planarity : 0.003 0.045 1362 Dihedral : 3.706 17.595 1061 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.22 % Allowed : 17.33 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 997 helix: 1.04 (0.24), residues: 519 sheet: -1.09 (0.46), residues: 107 loop : -0.36 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.001 0.000 HIS A 396 PHE 0.025 0.001 PHE A 759 TYR 0.016 0.001 TYR A 990 ARG 0.006 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7477 (mtm-85) REVERT: A 120 LYS cc_start: 0.7427 (mttp) cc_final: 0.7076 (mmtp) REVERT: A 140 ILE cc_start: 0.8126 (pt) cc_final: 0.7743 (pt) REVERT: A 297 LYS cc_start: 0.6758 (mtpp) cc_final: 0.6521 (mttp) REVERT: A 518 GLU cc_start: 0.8359 (pp20) cc_final: 0.7886 (pp20) REVERT: A 526 HIS cc_start: 0.7395 (m-70) cc_final: 0.7023 (m-70) REVERT: A 536 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7389 (ttm) REVERT: A 583 PHE cc_start: 0.7300 (m-80) cc_final: 0.6943 (m-80) REVERT: A 586 TYR cc_start: 0.7366 (m-80) cc_final: 0.7148 (m-80) REVERT: A 836 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5669 (p90) REVERT: A 1028 TRP cc_start: 0.7660 (t60) cc_final: 0.7069 (t60) outliers start: 19 outliers final: 16 residues processed: 136 average time/residue: 0.2487 time to fit residues: 43.8742 Evaluate side-chains 133 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 0.0170 chunk 39 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 0.0020 overall best weight: 0.5426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.178032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.135715 restraints weight = 8430.147| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.81 r_work: 0.3320 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7880 Z= 0.148 Angle : 0.486 5.641 10693 Z= 0.250 Chirality : 0.041 0.191 1259 Planarity : 0.003 0.045 1362 Dihedral : 3.657 17.856 1061 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.22 % Allowed : 17.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 997 helix: 1.15 (0.24), residues: 519 sheet: -1.02 (0.47), residues: 107 loop : -0.32 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 927 HIS 0.001 0.000 HIS A 15 PHE 0.024 0.001 PHE A 759 TYR 0.016 0.001 TYR A 990 ARG 0.007 0.000 ARG A 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.7466 (mttp) cc_final: 0.7064 (mmtp) REVERT: A 140 ILE cc_start: 0.8138 (pt) cc_final: 0.7749 (pt) REVERT: A 297 LYS cc_start: 0.6770 (mtpp) cc_final: 0.6514 (mttp) REVERT: A 332 ILE cc_start: 0.8920 (mm) cc_final: 0.8613 (mt) REVERT: A 518 GLU cc_start: 0.8468 (pp20) cc_final: 0.7975 (pp20) REVERT: A 536 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7393 (ttm) REVERT: A 583 PHE cc_start: 0.7313 (m-80) cc_final: 0.6965 (m-80) REVERT: A 714 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: A 836 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.5623 (p90) REVERT: A 1028 TRP cc_start: 0.7664 (t60) cc_final: 0.7069 (t60) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.2398 time to fit residues: 40.8814 Evaluate side-chains 129 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 836 TYR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 978 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.175842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134119 restraints weight = 8369.194| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.85 r_work: 0.3276 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7880 Z= 0.219 Angle : 0.518 7.378 10693 Z= 0.268 Chirality : 0.042 0.181 1259 Planarity : 0.004 0.047 1362 Dihedral : 3.777 18.090 1061 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.11 % Allowed : 17.92 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.27), residues: 997 helix: 1.06 (0.24), residues: 513 sheet: -1.16 (0.46), residues: 107 loop : -0.31 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 927 HIS 0.002 0.001 HIS A 15 PHE 0.023 0.001 PHE A 759 TYR 0.020 0.002 TYR A 586 ARG 0.010 0.001 ARG A 666 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4864.26 seconds wall clock time: 86 minutes 43.89 seconds (5203.89 seconds total)