Starting phenix.real_space_refine on Wed Mar 4 22:39:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3v_27165/03_2026/8d3v_27165_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3v_27165/03_2026/8d3v_27165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d3v_27165/03_2026/8d3v_27165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3v_27165/03_2026/8d3v_27165.map" model { file = "/net/cci-nas-00/data/ceres_data/8d3v_27165/03_2026/8d3v_27165_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3v_27165/03_2026/8d3v_27165_neut.cif" } resolution = 3.4 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8783 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6405 2.51 5 N 1679 2.21 5 O 1867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10011 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 960, 7402 Classifications: {'peptide': 960} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 40, 'TRANS': 919} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 960, 7402 Classifications: {'peptide': 960} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 40, 'TRANS': 919} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 7529 Chain: "B" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2352 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 267} Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 246 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 824 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 824 " occ=0.50 Time building chain proxies: 3.41, per 1000 atoms: 0.34 Number of scatterers: 10011 At special positions: 0 Unit cell: (140.4, 110.16, 129.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1867 8.00 N 1679 7.00 C 6405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 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 727.4 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 47.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.600A pdb=" N VAL A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.784A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.685A pdb=" N GLN A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 87 " --> pdb=" O CYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.554A pdb=" N TRP A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 140 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.753A pdb=" N LYS A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 removed outlier: 3.691A pdb=" N ASN A 153 " --> pdb=" O SER A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 153' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.686A pdb=" N THR A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 304 removed outlier: 3.560A pdb=" N GLU A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.527A pdb=" N ALA A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.724A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 405 through 416 removed outlier: 4.192A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.744A pdb=" N LEU A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 464 removed outlier: 4.011A pdb=" N ASN A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.552A pdb=" N LYS A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 657 through 661 removed outlier: 3.799A pdb=" N LYS A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 657 through 661' Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.597A pdb=" N GLN A 696 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 745 through 772 removed outlier: 3.941A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 769 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 786 Proline residue: A 779 - end of helix removed outlier: 3.563A pdb=" N ILE A 784 " --> pdb=" O PHE A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'A' and resid 807 through 815 removed outlier: 3.518A pdb=" N TYR A 814 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 815 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 844 removed outlier: 3.670A pdb=" N MET A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 866 removed outlier: 3.558A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 863 " --> pdb=" O TYR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.573A pdb=" N LEU A 873 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.683A pdb=" N VAL A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 904 " --> pdb=" O GLN A 900 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 937 Processing helix chain 'A' and resid 941 through 959 removed outlier: 4.197A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 968 removed outlier: 3.713A pdb=" N ALA A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.784A pdb=" N PHE A 979 " --> pdb=" O SER A 976 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N CYS A 980 " --> pdb=" O TRP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1002 removed outlier: 3.565A pdb=" N ARG A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'B' and resid 33 through 60 removed outlier: 3.542A pdb=" N PHE B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.524A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 112 No H-bonds generated for 'chain 'B' and resid 111 through 112' Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 231 through 235 removed outlier: 4.031A pdb=" N SER B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.962A pdb=" N TYR B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 57 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 11.955A pdb=" N GLN A 158 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LYS A 184 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.583A pdb=" N ASP A 187 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A 238 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS A 202 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS A 201 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.566A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL A 606 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 365 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N CYS A 653 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA A 681 " --> pdb=" O CYS A 653 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE A 655 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.666A pdb=" N MET A 381 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL A 378 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE A 582 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE A 545 " --> pdb=" O GLY A 577 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 579 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 482 through 484 Processing sheet with id=AA6, first strand: chain 'A' and resid 516 through 519 removed outlier: 5.723A pdb=" N LEU A 573 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 510 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 421 hydrogen bonds defined for protein. 1176 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: 1.83 Time building geometry restraints manager: 1.03 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: 3269 1.34 - 1.46: 2149 1.46 - 1.58: 4712 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 10218 Sorted by residual: bond pdb=" CG1 ILE A 691 " pdb=" CD1 ILE A 691 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.48e+00 bond pdb=" C ILE B 80 " pdb=" N PRO B 81 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 bond pdb=" N ASP B 120 " pdb=" CA ASP B 120 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" CB THR A 796 " pdb=" CG2 THR A 796 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.81e-01 bond pdb=" C THR B 28 " pdb=" N GLY B 29 " ideal model delta sigma weight residual 1.320 1.331 -0.011 1.26e-02 6.30e+03 7.37e-01 ... (remaining 10213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 13558 1.38 - 2.75: 227 2.75 - 4.13: 52 4.13 - 5.50: 13 5.50 - 6.88: 1 Bond angle restraints: 13851 Sorted by residual: angle pdb=" N GLY A 499 " pdb=" CA GLY A 499 " pdb=" C GLY A 499 " ideal model delta sigma weight residual 111.18 115.34 -4.16 1.54e+00 4.22e-01 7.31e+00 angle pdb=" N ILE B 80 " pdb=" CA ILE B 80 " pdb=" C ILE B 80 " ideal model delta sigma weight residual 108.88 114.28 -5.40 2.16e+00 2.14e-01 6.26e+00 angle pdb=" N GLY B 225 " pdb=" CA GLY B 225 " pdb=" C GLY B 225 " ideal model delta sigma weight residual 112.33 115.21 -2.88 1.21e+00 6.83e-01 5.67e+00 angle pdb=" C TRP B 32 " pdb=" N PHE B 33 " pdb=" CA PHE B 33 " ideal model delta sigma weight residual 122.58 117.83 4.75 2.07e+00 2.33e-01 5.26e+00 angle pdb=" N LEU A 308 " pdb=" CA LEU A 308 " pdb=" C LEU A 308 " ideal model delta sigma weight residual 113.12 110.38 2.74 1.25e+00 6.40e-01 4.81e+00 ... (remaining 13846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5525 17.87 - 35.73: 504 35.73 - 53.60: 90 53.60 - 71.47: 21 71.47 - 89.34: 11 Dihedral angle restraints: 6151 sinusoidal: 2466 harmonic: 3685 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 50.79 42.21 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA GLU B 23 " pdb=" C GLU B 23 " pdb=" N PHE B 24 " pdb=" CA PHE B 24 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ARG A 343 " pdb=" C ARG A 343 " pdb=" N LYS A 344 " pdb=" CA LYS A 344 " ideal model delta harmonic sigma weight residual 180.00 162.18 17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 872 0.028 - 0.057: 474 0.057 - 0.085: 139 0.085 - 0.114: 70 0.114 - 0.142: 15 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CA ILE A 640 " pdb=" N ILE A 640 " pdb=" C ILE A 640 " pdb=" CB ILE A 640 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 430 " pdb=" N ILE A 430 " pdb=" C ILE A 430 " pdb=" CB ILE A 430 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1567 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 272 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO A 273 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 79 " 0.011 2.00e-02 2.50e+03 1.12e-02 3.15e+00 pdb=" CG TRP A 79 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 79 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 79 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 79 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 79 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 79 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 79 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 79 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 79 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 684 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 685 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 685 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 685 " 0.024 5.00e-02 4.00e+02 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 162 2.69 - 3.25: 9819 3.25 - 3.80: 14828 3.80 - 4.35: 20212 4.35 - 4.90: 33319 Nonbonded interactions: 78340 Sorted by model distance: nonbonded pdb=" O VAL A1007 " pdb=" OG1 THR A1011 " model vdw 2.143 3.040 nonbonded pdb=" NE2 HIS A 199 " pdb=" O GLU A 469 " model vdw 2.247 3.120 nonbonded pdb=" OG SER A 509 " pdb=" OD1 ASN A 572 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLN A 846 " pdb=" OH TYR A 991 " model vdw 2.282 3.040 nonbonded pdb=" O PRO A 219 " pdb=" ND2 ASN A 231 " model vdw 2.286 3.120 ... (remaining 78335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 0.047 10220 Z= 0.115 Angle : 0.493 6.877 13855 Z= 0.266 Chirality : 0.040 0.142 1570 Planarity : 0.004 0.052 1785 Dihedral : 14.467 89.335 3779 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.13 (0.24), residues: 1272 helix: -0.44 (0.22), residues: 515 sheet: -1.47 (0.46), residues: 130 loop : -0.71 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 343 TYR 0.008 0.001 TYR A 859 PHE 0.022 0.001 PHE B 24 TRP 0.031 0.002 TRP A 79 HIS 0.001 0.000 HIS A 483 Details of bonding type rmsd covalent geometry : bond 0.00263 (10218) covalent geometry : angle 0.49342 (13851) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.63001 ( 4) hydrogen bonds : bond 0.25050 ( 421) hydrogen bonds : angle 8.40472 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.311 Fit side-chains REVERT: A 529 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7288 (mt0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0970 time to fit residues: 16.1135 Evaluate side-chains 98 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.0670 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN B 205 ASN B 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.173095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.137307 restraints weight = 19931.834| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 4.32 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10220 Z= 0.116 Angle : 0.535 6.779 13855 Z= 0.282 Chirality : 0.042 0.202 1570 Planarity : 0.004 0.050 1785 Dihedral : 4.062 19.571 1379 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.55 % Allowed : 5.58 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.54 (0.24), residues: 1272 helix: 0.37 (0.23), residues: 521 sheet: -1.52 (0.49), residues: 118 loop : -0.66 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 343 TYR 0.009 0.001 TYR A 121 PHE 0.017 0.001 PHE B 24 TRP 0.020 0.001 TRP A 79 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00245 (10218) covalent geometry : angle 0.53490 (13851) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.62057 ( 4) hydrogen bonds : bond 0.05161 ( 421) hydrogen bonds : angle 5.21467 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.322 Fit side-chains REVERT: A 148 MET cc_start: 0.7489 (mmp) cc_final: 0.7246 (mmp) REVERT: A 689 LEU cc_start: 0.8841 (tp) cc_final: 0.8637 (tp) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.0940 time to fit residues: 15.4612 Evaluate side-chains 105 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 108 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 HIS A 936 GLN B 140 ASN B 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.174147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138781 restraints weight = 19626.359| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.29 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10220 Z= 0.102 Angle : 0.482 6.696 13855 Z= 0.254 Chirality : 0.041 0.209 1570 Planarity : 0.004 0.050 1785 Dihedral : 3.942 19.439 1379 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.46 % Allowed : 8.50 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.23 (0.25), residues: 1272 helix: 0.81 (0.24), residues: 524 sheet: -1.33 (0.49), residues: 127 loop : -0.67 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1000 TYR 0.011 0.001 TYR A1013 PHE 0.015 0.001 PHE B 24 TRP 0.015 0.001 TRP A 79 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00227 (10218) covalent geometry : angle 0.48200 (13851) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.47784 ( 4) hydrogen bonds : bond 0.04058 ( 421) hydrogen bonds : angle 4.64039 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.356 Fit side-chains REVERT: A 105 TYR cc_start: 0.8986 (t80) cc_final: 0.8781 (t80) REVERT: A 204 ASP cc_start: 0.7527 (t0) cc_final: 0.7228 (p0) REVERT: A 336 LEU cc_start: 0.8884 (mt) cc_final: 0.8568 (mt) outliers start: 5 outliers final: 4 residues processed: 117 average time/residue: 0.0981 time to fit residues: 16.3530 Evaluate side-chains 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 42 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 ASN A 936 GLN B 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.167995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.132360 restraints weight = 20140.254| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.25 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10220 Z= 0.178 Angle : 0.547 6.873 13855 Z= 0.287 Chirality : 0.044 0.235 1570 Planarity : 0.004 0.052 1785 Dihedral : 4.259 19.587 1379 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.28 % Allowed : 10.05 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.47 (0.24), residues: 1272 helix: 0.62 (0.23), residues: 528 sheet: -1.67 (0.46), residues: 122 loop : -0.77 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 254 TYR 0.013 0.001 TYR A 121 PHE 0.017 0.002 PHE G 44 TRP 0.015 0.001 TRP A 79 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00442 (10218) covalent geometry : angle 0.54703 (13851) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.37704 ( 4) hydrogen bonds : bond 0.04477 ( 421) hydrogen bonds : angle 4.67499 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.361 Fit side-chains REVERT: A 204 ASP cc_start: 0.7529 (t0) cc_final: 0.7156 (p0) REVERT: A 738 MET cc_start: 0.7425 (ttt) cc_final: 0.6845 (ttt) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.0807 time to fit residues: 12.5404 Evaluate side-chains 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 50 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 ASN A 936 GLN B 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.171341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134172 restraints weight = 23553.099| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 4.70 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10220 Z= 0.107 Angle : 0.489 6.678 13855 Z= 0.256 Chirality : 0.042 0.222 1570 Planarity : 0.004 0.049 1785 Dihedral : 4.058 19.334 1379 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.10 % Allowed : 10.88 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.23 (0.24), residues: 1272 helix: 0.87 (0.24), residues: 527 sheet: -1.37 (0.46), residues: 127 loop : -0.72 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.008 0.001 TYR B 246 PHE 0.012 0.001 PHE G 44 TRP 0.014 0.001 TRP A 79 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00250 (10218) covalent geometry : angle 0.48900 (13851) SS BOND : bond 0.00089 ( 2) SS BOND : angle 0.31845 ( 4) hydrogen bonds : bond 0.03688 ( 421) hydrogen bonds : angle 4.40137 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.362 Fit side-chains REVERT: A 204 ASP cc_start: 0.7548 (t0) cc_final: 0.7241 (p0) REVERT: A 230 ARG cc_start: 0.7708 (mmt90) cc_final: 0.7204 (mtt180) REVERT: A 336 LEU cc_start: 0.8804 (mt) cc_final: 0.8545 (mt) REVERT: A 738 MET cc_start: 0.7286 (ttt) cc_final: 0.6742 (ttt) REVERT: B 121 MET cc_start: 0.5805 (OUTLIER) cc_final: 0.5566 (ttm) REVERT: G 31 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.7187 (t70) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 0.0775 time to fit residues: 11.7605 Evaluate side-chains 99 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 50 optimal weight: 0.0970 chunk 6 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 ASN A 936 GLN B 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.171064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.135221 restraints weight = 21184.970| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.42 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10220 Z= 0.117 Angle : 0.493 6.655 13855 Z= 0.258 Chirality : 0.042 0.221 1570 Planarity : 0.004 0.049 1785 Dihedral : 4.039 19.093 1379 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.28 % Allowed : 10.97 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.20 (0.24), residues: 1272 helix: 0.89 (0.23), residues: 530 sheet: -1.37 (0.46), residues: 127 loop : -0.71 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.009 0.001 TYR B 246 PHE 0.013 0.001 PHE G 44 TRP 0.012 0.001 TRP A 79 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00281 (10218) covalent geometry : angle 0.49295 (13851) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.30220 ( 4) hydrogen bonds : bond 0.03674 ( 421) hydrogen bonds : angle 4.33836 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.359 Fit side-chains REVERT: A 204 ASP cc_start: 0.7523 (t0) cc_final: 0.7215 (p0) REVERT: A 230 ARG cc_start: 0.7700 (mmt90) cc_final: 0.7207 (mtt180) REVERT: A 738 MET cc_start: 0.7433 (ttt) cc_final: 0.6874 (ttt) REVERT: B 59 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 121 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.5391 (ttm) REVERT: B 262 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: G 31 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7307 (t70) outliers start: 14 outliers final: 6 residues processed: 105 average time/residue: 0.0949 time to fit residues: 14.4081 Evaluate side-chains 101 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 52 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 121 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 ASN A 936 GLN B 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.170046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132987 restraints weight = 23300.877| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.64 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10220 Z= 0.127 Angle : 0.504 7.435 13855 Z= 0.263 Chirality : 0.042 0.227 1570 Planarity : 0.004 0.049 1785 Dihedral : 4.090 19.038 1379 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.55 % Allowed : 11.33 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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 (0.24), residues: 1272 helix: 0.90 (0.23), residues: 530 sheet: -1.36 (0.46), residues: 127 loop : -0.74 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 107 TYR 0.009 0.001 TYR A 121 PHE 0.013 0.001 PHE G 44 TRP 0.012 0.001 TRP A 79 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00309 (10218) covalent geometry : angle 0.50442 (13851) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.30000 ( 4) hydrogen bonds : bond 0.03725 ( 421) hydrogen bonds : angle 4.31462 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.330 Fit side-chains REVERT: A 204 ASP cc_start: 0.7565 (t0) cc_final: 0.7265 (p0) REVERT: A 230 ARG cc_start: 0.7694 (mmt90) cc_final: 0.7194 (mtt180) REVERT: B 59 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8183 (mp) REVERT: B 121 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5625 (ttm) REVERT: B 262 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: G 31 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.7235 (t70) outliers start: 17 outliers final: 9 residues processed: 106 average time/residue: 0.0826 time to fit residues: 13.3953 Evaluate side-chains 107 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 97 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 14 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 ASN A 872 ASN A 936 GLN B 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.171799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133900 restraints weight = 24426.401| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 5.00 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10220 Z= 0.100 Angle : 0.487 7.238 13855 Z= 0.254 Chirality : 0.041 0.220 1570 Planarity : 0.004 0.051 1785 Dihedral : 3.985 18.777 1379 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.10 % Allowed : 12.25 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1272 helix: 1.06 (0.24), residues: 530 sheet: -1.30 (0.46), residues: 127 loop : -0.67 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 107 TYR 0.007 0.001 TYR B 246 PHE 0.025 0.001 PHE A 663 TRP 0.012 0.001 TRP A 79 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00229 (10218) covalent geometry : angle 0.48664 (13851) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.64319 ( 4) hydrogen bonds : bond 0.03366 ( 421) hydrogen bonds : angle 4.19452 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.463 Fit side-chains REVERT: A 204 ASP cc_start: 0.7533 (t0) cc_final: 0.7321 (p0) REVERT: A 230 ARG cc_start: 0.7648 (mmt90) cc_final: 0.7122 (mtt180) REVERT: A 413 HIS cc_start: 0.3715 (t-90) cc_final: 0.3098 (t-170) REVERT: A 810 ILE cc_start: 0.8558 (mm) cc_final: 0.8323 (mm) REVERT: B 121 MET cc_start: 0.5786 (OUTLIER) cc_final: 0.5530 (ttm) REVERT: B 262 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: B 282 ASN cc_start: 0.8026 (m110) cc_final: 0.7790 (m-40) REVERT: G 31 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.7278 (t70) outliers start: 12 outliers final: 7 residues processed: 105 average time/residue: 0.0810 time to fit residues: 13.0201 Evaluate side-chains 102 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 65 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 72 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 113 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 674 ASN A 872 ASN A 936 GLN A1002 ASN B 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.174762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.138137 restraints weight = 24180.571| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 4.67 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10220 Z= 0.093 Angle : 0.477 7.667 13855 Z= 0.248 Chirality : 0.041 0.212 1570 Planarity : 0.004 0.052 1785 Dihedral : 3.849 18.338 1379 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.28 % Allowed : 12.80 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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 (0.25), residues: 1272 helix: 1.25 (0.24), residues: 528 sheet: -1.03 (0.47), residues: 132 loop : -0.64 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 107 TYR 0.006 0.001 TYR A 478 PHE 0.033 0.001 PHE A 663 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00206 (10218) covalent geometry : angle 0.47660 (13851) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.71964 ( 4) hydrogen bonds : bond 0.03085 ( 421) hydrogen bonds : angle 4.04573 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.399 Fit side-chains REVERT: A 204 ASP cc_start: 0.7542 (t0) cc_final: 0.7306 (p0) REVERT: A 230 ARG cc_start: 0.7618 (mmt90) cc_final: 0.6893 (mtt-85) REVERT: A 413 HIS cc_start: 0.3877 (t-90) cc_final: 0.3229 (t-170) REVERT: A 810 ILE cc_start: 0.8532 (mm) cc_final: 0.8311 (mm) REVERT: B 59 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8131 (mp) REVERT: B 262 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: G 31 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.7262 (t70) outliers start: 14 outliers final: 6 residues processed: 109 average time/residue: 0.0946 time to fit residues: 15.3468 Evaluate side-chains 108 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 123 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 ASN A 936 GLN A1002 ASN B 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.171162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127758 restraints weight = 29304.861| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.49 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10220 Z= 0.137 Angle : 0.517 7.416 13855 Z= 0.271 Chirality : 0.043 0.264 1570 Planarity : 0.004 0.053 1785 Dihedral : 4.002 18.417 1379 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.10 % Allowed : 12.80 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.00 (0.24), residues: 1272 helix: 1.10 (0.23), residues: 529 sheet: -1.07 (0.47), residues: 132 loop : -0.68 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 107 TYR 0.010 0.001 TYR A 121 PHE 0.035 0.001 PHE A 663 TRP 0.012 0.001 TRP B 32 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00332 (10218) covalent geometry : angle 0.51678 (13851) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.56267 ( 4) hydrogen bonds : bond 0.03612 ( 421) hydrogen bonds : angle 4.14415 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.429 Fit side-chains REVERT: A 204 ASP cc_start: 0.7558 (t0) cc_final: 0.7259 (p0) REVERT: A 230 ARG cc_start: 0.7606 (mmt90) cc_final: 0.7010 (mtt-85) REVERT: A 413 HIS cc_start: 0.3716 (t-90) cc_final: 0.3072 (t-170) REVERT: B 59 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 262 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7103 (tm-30) outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 0.0951 time to fit residues: 15.2529 Evaluate side-chains 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 1002 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain G residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 872 ASN A 936 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.171850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135578 restraints weight = 23586.682| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.60 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.249 10220 Z= 0.273 Angle : 0.988 59.199 13855 Z= 0.610 Chirality : 0.066 1.528 1570 Planarity : 0.006 0.106 1785 Dihedral : 4.036 20.668 1379 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.19 % Rotamer: Outliers : 1.01 % Allowed : 12.80 % Favored : 86.20 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 1.64 % 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: -0.01 (0.24), residues: 1272 helix: 1.09 (0.23), residues: 528 sheet: -1.06 (0.47), residues: 132 loop : -0.69 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.010 0.001 TYR A 121 PHE 0.031 0.001 PHE A 663 TRP 0.011 0.001 TRP B 32 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00516 (10218) covalent geometry : angle 0.98786 (13851) SS BOND : bond 0.00072 ( 2) SS BOND : angle 0.49880 ( 4) hydrogen bonds : bond 0.03571 ( 421) hydrogen bonds : angle 4.16310 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2049.85 seconds wall clock time: 35 minutes 54.71 seconds (2154.71 seconds total)