Starting phenix.real_space_refine on Sun Jun 15 05:13:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3v_27165/06_2025/8d3v_27165_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3v_27165/06_2025/8d3v_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_27165/06_2025/8d3v_27165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3v_27165/06_2025/8d3v_27165.map" model { file = "/net/cci-nas-00/data/ceres_data/8d3v_27165/06_2025/8d3v_27165_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3v_27165/06_2025/8d3v_27165_neut.cif" } resolution = 3.4 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= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'PHE:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, '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: {'PHE:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, '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: 9.30, per 1000 atoms: 0.93 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: 2.23 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.41 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: 3.57 Time building geometry restraints manager: 2.69 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.480 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- 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 (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: -1.13 (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 TRP 0.031 0.002 TRP A 79 HIS 0.001 0.000 HIS A 483 PHE 0.022 0.001 PHE B 24 TYR 0.008 0.001 TYR A 859 ARG 0.006 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.25050 ( 421) hydrogen bonds : angle 8.40472 ( 1176) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.63001 ( 4) covalent geometry : bond 0.00263 (10218) covalent geometry : angle 0.49342 (13851) *********************** 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 : 1.068 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: 0.2250 time to fit residues: 37.3159 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 : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.0000 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- 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 610 HIS ** 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 = 0.3815 r_free = 0.3815 target = 0.166918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.122178 restraints weight = 25723.769| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.72 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10220 Z= 0.215 Angle : 0.610 7.132 13855 Z= 0.323 Chirality : 0.046 0.216 1570 Planarity : 0.005 0.055 1785 Dihedral : 4.488 21.604 1379 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.73 % Allowed : 6.49 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.94 (0.24), residues: 1272 helix: 0.01 (0.22), residues: 522 sheet: -1.73 (0.48), residues: 120 loop : -0.83 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 79 HIS 0.006 0.001 HIS G 31 PHE 0.018 0.002 PHE A 783 TYR 0.017 0.002 TYR A 121 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.06074 ( 421) hydrogen bonds : angle 5.40038 ( 1176) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.60624 ( 4) covalent geometry : bond 0.00524 (10218) covalent geometry : angle 0.60965 (13851) *********************** 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 110 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.816 Fit side-chains REVERT: A 529 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7176 (mt0) outliers start: 8 outliers final: 8 residues processed: 103 average time/residue: 0.3108 time to fit residues: 48.0073 Evaluate side-chains 102 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 377 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 GLN B 140 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 = 0.3871 r_free = 0.3871 target = 0.171952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135268 restraints weight = 26304.027| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 5.01 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10220 Z= 0.112 Angle : 0.508 6.888 13855 Z= 0.268 Chirality : 0.042 0.215 1570 Planarity : 0.004 0.050 1785 Dihedral : 4.214 20.107 1379 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.46 % Allowed : 8.59 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.56 (0.24), residues: 1272 helix: 0.52 (0.23), residues: 525 sheet: -1.78 (0.47), residues: 122 loop : -0.77 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.004 0.001 HIS G 31 PHE 0.014 0.001 PHE B 24 TYR 0.007 0.001 TYR B 246 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 421) hydrogen bonds : angle 4.80225 ( 1176) SS BOND : bond 0.00051 ( 2) SS BOND : angle 0.38955 ( 4) covalent geometry : bond 0.00253 (10218) covalent geometry : angle 0.50782 (13851) *********************** 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 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 1.012 Fit side-chains REVERT: A 204 ASP cc_start: 0.7396 (t0) cc_final: 0.7058 (p0) REVERT: A 336 LEU cc_start: 0.8896 (mt) cc_final: 0.8608 (mt) outliers start: 5 outliers final: 4 residues processed: 101 average time/residue: 0.2042 time to fit residues: 30.1648 Evaluate side-chains 95 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 25 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 0.0060 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 HIS B 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.171524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.135327 restraints weight = 21335.001| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 4.47 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1466 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= 0.101 Angle : 0.483 6.741 13855 Z= 0.254 Chirality : 0.041 0.221 1570 Planarity : 0.004 0.049 1785 Dihedral : 4.040 19.591 1379 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.46 % Allowed : 10.69 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.31 (0.25), residues: 1272 helix: 0.81 (0.24), residues: 527 sheet: -1.66 (0.47), residues: 122 loop : -0.73 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 79 HIS 0.004 0.001 HIS G 31 PHE 0.013 0.001 PHE B 24 TYR 0.015 0.001 TYR A1013 ARG 0.006 0.000 ARG A 254 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 421) hydrogen bonds : angle 4.48986 ( 1176) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.34099 ( 4) covalent geometry : bond 0.00228 (10218) covalent geometry : angle 0.48353 (13851) *********************** 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 106 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 1.026 Fit side-chains REVERT: A 204 ASP cc_start: 0.7415 (t0) cc_final: 0.7053 (p0) REVERT: A 230 ARG cc_start: 0.7720 (mmt90) cc_final: 0.7252 (mtt180) REVERT: A 336 LEU cc_start: 0.8890 (mt) cc_final: 0.8644 (mt) outliers start: 5 outliers final: 3 residues processed: 103 average time/residue: 0.2140 time to fit residues: 31.9305 Evaluate side-chains 100 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 167 TYR 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 69 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 ASN G 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.168482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129893 restraints weight = 25503.818| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.98 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10220 Z= 0.182 Angle : 0.553 6.933 13855 Z= 0.291 Chirality : 0.044 0.237 1570 Planarity : 0.004 0.052 1785 Dihedral : 4.369 19.912 1379 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.28 % Allowed : 10.60 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.54 (0.24), residues: 1272 helix: 0.61 (0.23), residues: 529 sheet: -1.80 (0.45), residues: 122 loop : -0.84 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 79 HIS 0.010 0.001 HIS G 31 PHE 0.017 0.002 PHE G 44 TYR 0.014 0.001 TYR A 121 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 421) hydrogen bonds : angle 4.59802 ( 1176) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.37937 ( 4) covalent geometry : bond 0.00451 (10218) covalent geometry : angle 0.55339 (13851) *********************** 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 109 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.100 Fit side-chains REVERT: A 336 LEU cc_start: 0.8822 (mt) cc_final: 0.8606 (mt) REVERT: A 936 GLN cc_start: 0.7510 (pt0) cc_final: 0.7172 (pt0) REVERT: B 262 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7015 (tm-30) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 0.2349 time to fit residues: 36.5665 Evaluate side-chains 100 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 214 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 270 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 2 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 110 optimal weight: 0.0870 chunk 114 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 GLN B 282 ASN 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 = 0.171818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.135688 restraints weight = 18547.770| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 4.19 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10220 Z= 0.097 Angle : 0.480 7.063 13855 Z= 0.252 Chirality : 0.041 0.217 1570 Planarity : 0.004 0.047 1785 Dihedral : 4.048 19.409 1379 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.82 % Allowed : 11.61 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.19 (0.25), residues: 1272 helix: 0.96 (0.24), residues: 527 sheet: -1.44 (0.46), residues: 127 loop : -0.73 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.002 0.000 HIS G 31 PHE 0.011 0.001 PHE G 49 TYR 0.007 0.001 TYR B 254 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 421) hydrogen bonds : angle 4.28367 ( 1176) SS BOND : bond 0.00075 ( 2) SS BOND : angle 0.32051 ( 4) covalent geometry : bond 0.00218 (10218) covalent geometry : angle 0.48006 (13851) *********************** 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 104 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.272 Fit side-chains REVERT: A 204 ASP cc_start: 0.7344 (t0) cc_final: 0.7032 (p0) REVERT: A 230 ARG cc_start: 0.7716 (mmt90) cc_final: 0.7226 (mtt180) REVERT: A 336 LEU cc_start: 0.8529 (mt) cc_final: 0.8277 (mt) REVERT: B 262 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7051 (tm-30) REVERT: B 282 ASN cc_start: 0.7950 (m110) cc_final: 0.7711 (m-40) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.2531 time to fit residues: 39.3528 Evaluate side-chains 96 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 262 GLN 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 104 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.169578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131726 restraints weight = 16959.248| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.12 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1646 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= 0.136 Angle : 0.506 7.351 13855 Z= 0.265 Chirality : 0.043 0.234 1570 Planarity : 0.004 0.048 1785 Dihedral : 4.153 19.209 1379 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.10 % Allowed : 11.43 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.26 (0.24), residues: 1272 helix: 0.88 (0.23), residues: 530 sheet: -1.43 (0.46), residues: 127 loop : -0.77 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS A 388 PHE 0.014 0.001 PHE G 44 TYR 0.010 0.001 TYR A 121 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 421) hydrogen bonds : angle 4.32982 ( 1176) SS BOND : bond 0.00463 ( 2) SS BOND : angle 0.89099 ( 4) covalent geometry : bond 0.00332 (10218) covalent geometry : angle 0.50585 (13851) *********************** 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 107 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.185 Fit side-chains REVERT: A 204 ASP cc_start: 0.7381 (t0) cc_final: 0.7022 (p0) REVERT: A 230 ARG cc_start: 0.7714 (mmt90) cc_final: 0.7234 (mtt180) REVERT: A 336 LEU cc_start: 0.8748 (mt) cc_final: 0.8472 (mt) REVERT: B 59 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 262 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.6994 (tm-30) outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.2037 time to fit residues: 31.9279 Evaluate side-chains 103 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 679 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 ASN ** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.170776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.128477 restraints weight = 30383.910| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.47 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 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 = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10220 Z= 0.103 Angle : 0.485 7.321 13855 Z= 0.255 Chirality : 0.042 0.229 1570 Planarity : 0.004 0.047 1785 Dihedral : 4.069 19.144 1379 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.01 % Allowed : 11.97 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.13 (0.24), residues: 1272 helix: 1.02 (0.24), residues: 530 sheet: -1.37 (0.46), residues: 127 loop : -0.74 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.002 0.001 HIS A 413 PHE 0.012 0.001 PHE A 663 TYR 0.007 0.001 TYR B 246 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 421) hydrogen bonds : angle 4.23366 ( 1176) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.62443 ( 4) covalent geometry : bond 0.00238 (10218) covalent geometry : angle 0.48495 (13851) *********************** 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 107 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.052 Fit side-chains REVERT: A 204 ASP cc_start: 0.7370 (t0) cc_final: 0.7070 (p0) REVERT: A 230 ARG cc_start: 0.7654 (mmt90) cc_final: 0.7210 (mtt180) REVERT: A 336 LEU cc_start: 0.8785 (mt) cc_final: 0.8502 (mt) REVERT: A 413 HIS cc_start: 0.3861 (t-90) cc_final: 0.3139 (t-170) REVERT: B 59 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8476 (mp) REVERT: B 262 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7129 (tm-30) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.1976 time to fit residues: 30.4918 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 : 1.137 ------------------------------------------------------------------------------- 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 679 VAL 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 167 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 262 GLN 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 73 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 124 optimal weight: 0.0370 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 674 ASN A 936 GLN A1002 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 = 0.171787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129514 restraints weight = 31994.296| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.51 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1793 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 : 0.474 7.238 13855 Z= 0.248 Chirality : 0.041 0.231 1570 Planarity : 0.004 0.053 1785 Dihedral : 3.979 18.739 1379 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.01 % Allowed : 12.34 % 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 (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: -0.02 (0.25), residues: 1272 helix: 1.17 (0.24), residues: 529 sheet: -1.34 (0.46), residues: 127 loop : -0.72 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 32 HIS 0.002 0.001 HIS A 388 PHE 0.014 0.001 PHE A 663 TYR 0.007 0.001 TYR B 246 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 421) hydrogen bonds : angle 4.09050 ( 1176) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.56873 ( 4) covalent geometry : bond 0.00232 (10218) covalent geometry : angle 0.47408 (13851) *********************** 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: 11 poor density : 105 time to evaluate : 1.014 Fit side-chains REVERT: A 204 ASP cc_start: 0.7341 (t0) cc_final: 0.7063 (p0) REVERT: A 230 ARG cc_start: 0.7594 (mmt90) cc_final: 0.7143 (mtt180) REVERT: A 336 LEU cc_start: 0.8762 (mt) cc_final: 0.8488 (mt) REVERT: A 413 HIS cc_start: 0.3573 (t-90) cc_final: 0.2909 (t-170) REVERT: B 59 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8405 (mp) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.1881 time to fit residues: 31.1936 Evaluate side-chains 107 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 A residue 737 ASP Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 214 THR 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 116 optimal weight: 3.9990 chunk 34 optimal weight: 0.0030 chunk 2 optimal weight: 0.0270 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.0070 chunk 35 optimal weight: 0.9990 overall best weight: 0.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 936 GLN A1002 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.174245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.138555 restraints weight = 21133.795| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 4.40 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10220 Z= 0.093 Angle : 0.476 7.179 13855 Z= 0.251 Chirality : 0.041 0.249 1570 Planarity : 0.004 0.054 1785 Dihedral : 3.896 18.620 1379 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.91 % Allowed : 12.80 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.12 (0.25), residues: 1272 helix: 1.32 (0.24), residues: 527 sheet: -1.28 (0.46), residues: 127 loop : -0.67 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.002 0.000 HIS A 388 PHE 0.043 0.001 PHE A 663 TYR 0.006 0.001 TYR B 254 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 421) hydrogen bonds : angle 4.02794 ( 1176) SS BOND : bond 0.00052 ( 2) SS BOND : angle 0.50019 ( 4) covalent geometry : bond 0.00199 (10218) covalent geometry : angle 0.47557 (13851) ********************** 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 114 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 1.041 Fit side-chains REVERT: A 204 ASP cc_start: 0.7315 (t0) cc_final: 0.7049 (p0) REVERT: A 230 ARG cc_start: 0.7624 (mmt90) cc_final: 0.7337 (mtt180) REVERT: A 307 TRP cc_start: 0.6925 (t60) cc_final: 0.5257 (t60) REVERT: A 336 LEU cc_start: 0.8888 (mt) cc_final: 0.8604 (mt) REVERT: A 413 HIS cc_start: 0.3680 (t-90) cc_final: 0.3026 (t-170) REVERT: A 810 ILE cc_start: 0.8616 (mm) cc_final: 0.8372 (mm) REVERT: B 59 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8264 (mp) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.2129 time to fit residues: 34.0777 Evaluate side-chains 111 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 936 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 167 TYR 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 17 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 936 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.173540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.137286 restraints weight = 22410.576| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 4.53 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10220 Z= 0.094 Angle : 0.471 7.274 13855 Z= 0.247 Chirality : 0.041 0.229 1570 Planarity : 0.004 0.053 1785 Dihedral : 3.875 18.352 1379 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.82 % Allowed : 12.89 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1272 helix: 1.33 (0.24), residues: 527 sheet: -1.23 (0.46), residues: 127 loop : -0.64 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 79 HIS 0.002 0.001 HIS A 388 PHE 0.041 0.001 PHE A 663 TYR 0.006 0.001 TYR A 121 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 421) hydrogen bonds : angle 4.00944 ( 1176) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.47209 ( 4) covalent geometry : bond 0.00213 (10218) covalent geometry : angle 0.47109 (13851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4615.71 seconds wall clock time: 82 minutes 41.23 seconds (4961.23 seconds total)