Starting phenix.real_space_refine on Fri Sep 11 15:05:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egg_31116/09_2026/7egg_31116.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egg_31116/09_2026/7egg_31116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7egg_31116/09_2026/7egg_31116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egg_31116/09_2026/7egg_31116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7egg_31116/09_2026/7egg_31116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egg_31116/09_2026/7egg_31116.map" } resolution = 2.77 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= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6374 2.51 5 N 1737 2.21 5 O 1903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10062 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1271 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4376 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 524} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1137 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 134} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 112} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 108} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 720 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 6, 'TRANS': 83} Chain breaks: 1 Chain: "L" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Time building chain proxies: 2.07, per 1000 atoms: 0.21 Number of scatterers: 10062 At special positions: 0 Unit cell: (113.16, 96.76, 104.96, 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 48 16.00 O 1903 8.00 N 1737 7.00 C 6374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 357.3 milliseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2406 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 45.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'D' and resid 842 through 857 removed outlier: 3.739A pdb=" N SER D 846 " --> pdb=" O GLY D 842 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 852 " --> pdb=" O GLU D 848 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 853 " --> pdb=" O SER D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 874 through 886 removed outlier: 3.682A pdb=" N ARG D 880 " --> pdb=" O ALA D 876 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 885 " --> pdb=" O ARG D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 898 through 922 removed outlier: 3.638A pdb=" N SER D 903 " --> pdb=" O VAL D 899 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN D 912 " --> pdb=" O GLN D 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS D 916 " --> pdb=" O ASN D 912 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 920 " --> pdb=" O LYS D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 970 removed outlier: 3.891A pdb=" N GLN D 943 " --> pdb=" O ASP D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1066 removed outlier: 3.619A pdb=" N LEU D1063 " --> pdb=" O ASN D1059 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS D1066 " --> pdb=" O ASP D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1083 Processing helix chain 'D' and resid 1084 through 1085 No H-bonds generated for 'chain 'D' and resid 1084 through 1085' Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 213 through 227 removed outlier: 3.841A pdb=" N SER E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.811A pdb=" N ALA E 234 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU E 235 " --> pdb=" O CYS E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 254 removed outlier: 3.696A pdb=" N LEU E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 269 through 271 No H-bonds generated for 'chain 'E' and resid 269 through 271' Processing helix chain 'E' and resid 272 through 274 No H-bonds generated for 'chain 'E' and resid 272 through 274' Processing helix chain 'E' and resid 275 through 285 Processing helix chain 'E' and resid 287 through 292 removed outlier: 3.802A pdb=" N MET E 291 " --> pdb=" O LYS E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 303 removed outlier: 3.709A pdb=" N THR E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 319 removed outlier: 4.309A pdb=" N LEU E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 327 removed outlier: 3.511A pdb=" N ASN E 326 " --> pdb=" O GLU E 323 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN E 327 " --> pdb=" O LYS E 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 327' Processing helix chain 'E' and resid 328 through 337 Processing helix chain 'E' and resid 348 through 356 removed outlier: 3.906A pdb=" N ALA E 354 " --> pdb=" O GLN E 350 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET E 355 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 449 removed outlier: 3.536A pdb=" N LYS E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET E 442 " --> pdb=" O LEU E 438 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 446 " --> pdb=" O MET E 442 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 516 removed outlier: 3.700A pdb=" N LEU E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 516 " --> pdb=" O ASP E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 527 Processing helix chain 'E' and resid 741 through 745 removed outlier: 4.192A pdb=" N GLU E 745 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 768 Processing helix chain 'F' and resid 15 through 25 removed outlier: 3.750A pdb=" N MET F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 61 removed outlier: 3.556A pdb=" N LEU F 39 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR F 40 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 44 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS F 56 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 78 removed outlier: 4.195A pdb=" N ILE F 71 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 removed outlier: 3.530A pdb=" N THR F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 49 removed outlier: 3.511A pdb=" N HIS H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG H 33 " --> pdb=" O TYR H 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 37 " --> pdb=" O ARG H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 83 removed outlier: 3.517A pdb=" N LYS H 77 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 103 through 105 No H-bonds generated for 'chain 'H' and resid 103 through 105' Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.872A pdb=" N LYS H 112 " --> pdb=" O PRO H 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 26 removed outlier: 3.574A pdb=" N MET I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 62 removed outlier: 4.412A pdb=" N ILE I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN I 37 " --> pdb=" O PRO I 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP I 53 " --> pdb=" O THR I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 77 removed outlier: 3.552A pdb=" N VAL I 71 " --> pdb=" O ASP I 67 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 100 removed outlier: 3.675A pdb=" N ASP I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 123 Processing helix chain 'J' and resid 131 through 141 removed outlier: 3.689A pdb=" N TYR J 137 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 177 Processing helix chain 'J' and resid 196 through 204 Proline residue: J 202 - end of helix Processing helix chain 'L' and resid 61 through 71 removed outlier: 3.952A pdb=" N VAL L 70 " --> pdb=" O LEU L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 106 Processing helix chain 'L' and resid 112 through 123 removed outlier: 3.715A pdb=" N VAL L 116 " --> pdb=" O GLU L 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS L 119 " --> pdb=" O ASP L 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 934 through 936 Processing sheet with id=AA2, first strand: chain 'D' and resid 1056 through 1058 removed outlier: 6.394A pdb=" N THR D1056 " --> pdb=" O GLN L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 308 through 310 Processing sheet with id=AA4, first strand: chain 'E' and resid 782 through 785 removed outlier: 3.726A pdb=" N GLY E 795 " --> pdb=" O TYR E 464 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE E 461 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 478 removed outlier: 3.998A pdb=" N THR E 493 " --> pdb=" O PHE E 489 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 504 through 507 removed outlier: 3.719A pdb=" N SER E 506 " --> pdb=" O THR E 532 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N THR E 532 " --> pdb=" O SER E 506 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 546 through 550 removed outlier: 3.505A pdb=" N SER E 562 " --> pdb=" O THR E 566 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR E 566 " --> pdb=" O SER E 562 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 579 " --> pdb=" O LEU E 569 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 588 through 593 Processing sheet with id=AA9, first strand: chain 'E' and resid 634 through 635 removed outlier: 3.615A pdb=" N ARG E 663 " --> pdb=" O LEU E 653 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP E 655 " --> pdb=" O CYS E 661 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N CYS E 661 " --> pdb=" O ASP E 655 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 672 through 677 removed outlier: 6.385A pdb=" N VAL E 693 " --> pdb=" O GLU E 706 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU E 706 " --> pdb=" O VAL E 693 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU E 695 " --> pdb=" O VAL E 704 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 714 through 719 removed outlier: 4.181A pdb=" N THR E 734 " --> pdb=" O SER E 730 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 735 " --> pdb=" O THR E 772 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR E 772 " --> pdb=" O VAL E 735 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU E 737 " --> pdb=" O LEU E 770 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 86 through 88 415 hydrogen bonds defined for protein. 1215 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: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1688 1.28 - 1.41: 2540 1.41 - 1.55: 5954 1.55 - 1.68: 16 1.68 - 1.81: 78 Bond restraints: 10276 Sorted by residual: bond pdb=" C ASN H 28 " pdb=" O ASN H 28 " ideal model delta sigma weight residual 1.237 1.149 0.088 1.17e-02 7.31e+03 5.64e+01 bond pdb=" C ASP H 27 " pdb=" O ASP H 27 " ideal model delta sigma weight residual 1.237 1.151 0.085 1.19e-02 7.06e+03 5.14e+01 bond pdb=" C LEU H 31 " pdb=" O LEU H 31 " ideal model delta sigma weight residual 1.237 1.162 0.075 1.19e-02 7.06e+03 3.96e+01 bond pdb=" C LEU E 524 " pdb=" O LEU E 524 " ideal model delta sigma weight residual 1.237 1.303 -0.066 1.17e-02 7.31e+03 3.22e+01 bond pdb=" C TYR J 193 " pdb=" O TYR J 193 " ideal model delta sigma weight residual 1.242 1.196 0.046 1.00e-02 1.00e+04 2.08e+01 ... (remaining 10271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 13335 2.68 - 5.36: 515 5.36 - 8.03: 50 8.03 - 10.71: 12 10.71 - 13.39: 2 Bond angle restraints: 13914 Sorted by residual: angle pdb=" N THR E 756 " pdb=" CA THR E 756 " pdb=" C THR E 756 " ideal model delta sigma weight residual 113.50 103.21 10.29 1.23e+00 6.61e-01 7.01e+01 angle pdb=" N ALA H 32 " pdb=" CA ALA H 32 " pdb=" C ALA H 32 " ideal model delta sigma weight residual 111.07 102.26 8.81 1.07e+00 8.73e-01 6.78e+01 angle pdb=" N ASP H 27 " pdb=" CA ASP H 27 " pdb=" C ASP H 27 " ideal model delta sigma weight residual 111.36 102.78 8.58 1.09e+00 8.42e-01 6.19e+01 angle pdb=" N PRO E 762 " pdb=" CA PRO E 762 " pdb=" C PRO E 762 " ideal model delta sigma weight residual 114.27 124.27 -10.00 1.35e+00 5.49e-01 5.49e+01 angle pdb=" C ASP J 148 " pdb=" N PRO J 149 " pdb=" CA PRO J 149 " ideal model delta sigma weight residual 119.05 125.82 -6.77 1.11e+00 8.12e-01 3.72e+01 ... (remaining 13909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5555 17.58 - 35.17: 565 35.17 - 52.75: 121 52.75 - 70.33: 10 70.33 - 87.92: 7 Dihedral angle restraints: 6258 sinusoidal: 2557 harmonic: 3701 Sorted by residual: dihedral pdb=" C GLU H 51 " pdb=" N GLU H 51 " pdb=" CA GLU H 51 " pdb=" CB GLU H 51 " ideal model delta harmonic sigma weight residual -122.60 -106.45 -16.15 0 2.50e+00 1.60e-01 4.17e+01 dihedral pdb=" CA PRO H 156 " pdb=" C PRO H 156 " pdb=" N HIS H 157 " pdb=" CA HIS H 157 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA TYR E 470 " pdb=" C TYR E 470 " pdb=" N GLN E 471 " pdb=" CA GLN E 471 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 6255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1380 0.118 - 0.236: 129 0.236 - 0.354: 35 0.354 - 0.472: 5 0.472 - 0.590: 2 Chirality restraints: 1551 Sorted by residual: chirality pdb=" CA PRO H 25 " pdb=" N PRO H 25 " pdb=" C PRO H 25 " pdb=" CB PRO H 25 " both_signs ideal model delta sigma weight residual False 2.72 2.13 0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CA ASN H 28 " pdb=" N ASN H 28 " pdb=" C ASN H 28 " pdb=" CB ASN H 28 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" CA GLU H 51 " pdb=" N GLU H 51 " pdb=" C GLU H 51 " pdb=" CB GLU H 51 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 1548 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 769 " 0.022 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C LEU E 769 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU E 769 " 0.030 2.00e-02 2.50e+03 pdb=" N LEU E 770 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 92 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C ILE L 92 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE L 92 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU L 93 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER J 147 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C SER J 147 " 0.056 2.00e-02 2.50e+03 pdb=" O SER J 147 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP J 148 " -0.019 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2183 2.78 - 3.31: 9049 3.31 - 3.84: 16913 3.84 - 4.37: 21839 4.37 - 4.90: 35515 Nonbonded interactions: 85499 Sorted by model distance: nonbonded pdb=" N ASP L 79 " pdb=" OD1 ASP L 79 " model vdw 2.248 3.120 nonbonded pdb=" OG SER E 562 " pdb=" OD1 ASP E 564 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR D1080 " pdb=" OD2 ASP E 606 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR E 479 " pdb=" O ASP E 481 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASP E 732 " pdb=" OG1 THR E 734 " model vdw 2.313 3.040 ... (remaining 85494 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.740 Find NCS groups from input model: 0.060 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:9.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.008 0.088 10276 Z= 0.502 Angle : 1.131 13.388 13914 Z= 0.764 Chirality : 0.082 0.590 1551 Planarity : 0.008 0.076 1802 Dihedral : 14.566 87.919 3852 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 3.51 % Allowed : 6.49 % Favored : 90.00 % Cbeta Deviations : 1.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.21), residues: 1233 helix: -2.37 (0.19), residues: 567 sheet: -1.37 (0.41), residues: 140 loop : -1.94 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 787 TYR 0.037 0.002 TYR E 274 PHE 0.028 0.002 PHE E 600 TRP 0.028 0.002 TRP E 612 HIS 0.005 0.001 HIS J 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.50 (10276) covalent geometry : angle 1.13125 / 0.76 (13914) hydrogen bonds : bond 0.24607 / 16.49 ( 415) hydrogen bonds : angle 8.94623 / 6.35 ( 1215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 272 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 953 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7114 (mp) REVERT: D 960 GLU cc_start: 0.6250 (OUTLIER) cc_final: 0.5966 (tt0) REVERT: E 320 HIS cc_start: 0.7477 (t70) cc_final: 0.7183 (t70) REVERT: E 434 ASP cc_start: 0.7223 (m-30) cc_final: 0.6982 (OUTLIER) REVERT: J 192 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.5721 (mptt) outliers start: 39 outliers final: 13 residues processed: 300 average time/residue: 0.6012 time to fit residues: 193.0004 Evaluate side-chains 225 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 952 GLN Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain D residue 960 GLU Chi-restraints excluded: chain D residue 965 ILE Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 164 SER Chi-restraints excluded: chain J residue 174 CYS Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 113 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 856 ASN D 936 GLN E 223 HIS E 232 HIS E 254 ASN E 256 HIS E 268 HIS E 326 ASN E 350 GLN E 351 GLN E 616 HIS E 636 HIS E 640 ASN E 673 HIS F 52 GLN F 89 GLN F 119 ASN H 145 HIS I 21 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN J 160 GLN J 210 ASN L 73 ASN L 117 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.149825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.124627 restraints weight = 12670.499| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.87 r_work: 0.3415 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10276 Z= 0.136 Angle : 0.593 10.141 13914 Z= 0.310 Chirality : 0.042 0.145 1551 Planarity : 0.006 0.064 1802 Dihedral : 7.020 75.739 1397 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 4.77 % Allowed : 16.04 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.22), residues: 1233 helix: -1.01 (0.21), residues: 567 sheet: -0.57 (0.43), residues: 133 loop : -1.51 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1071 TYR 0.012 0.001 TYR E 274 PHE 0.014 0.001 PHE E 600 TRP 0.030 0.002 TRP E 612 HIS 0.005 0.001 HIS L 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10276) covalent geometry : angle 0.59266 / 0.31 (13914) hydrogen bonds : bond 0.04594 / 3.02 ( 415) hydrogen bonds : angle 4.49273 / 3.22 ( 1215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: D 960 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.6076 (tm-30) REVERT: D 967 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.5151 (tpp) REVERT: E 226 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: E 265 GLU cc_start: 0.8442 (tp30) cc_final: 0.8233 (tt0) REVERT: E 434 ASP cc_start: 0.7620 (m-30) cc_final: 0.6953 (t0) REVERT: E 536 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8828 (tp) REVERT: F 56 LYS cc_start: 0.8727 (mttm) cc_final: 0.8334 (mttt) REVERT: F 76 LYS cc_start: 0.8612 (tttm) cc_final: 0.8296 (ttmm) REVERT: F 128 ASP cc_start: 0.8421 (t0) cc_final: 0.8048 (t70) REVERT: H 117 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6979 (mpt) REVERT: I 94 ASP cc_start: 0.8348 (t70) cc_final: 0.8062 (t70) REVERT: J 199 ASP cc_start: 0.8314 (m-30) cc_final: 0.7765 (m-30) REVERT: L 83 MET cc_start: 0.8519 (tpp) cc_final: 0.8206 (ttp) outliers start: 53 outliers final: 21 residues processed: 264 average time/residue: 0.6000 time to fit residues: 169.0143 Evaluate side-chains 238 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 938 SER Chi-restraints excluded: chain D residue 952 GLN Chi-restraints excluded: chain D residue 960 GLU Chi-restraints excluded: chain D residue 965 ILE Chi-restraints excluded: chain D residue 967 MET Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 273 CYS Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 79 ASP Chi-restraints excluded: chain L residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 856 ASN E 232 HIS ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN E 618 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN J 210 ASN L 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125273 restraints weight = 12542.717| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.82 r_work: 0.3430 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10276 Z= 0.122 Angle : 0.553 10.068 13914 Z= 0.283 Chirality : 0.041 0.145 1551 Planarity : 0.005 0.057 1802 Dihedral : 5.973 74.550 1380 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 4.50 % Allowed : 19.37 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.90 (0.23), residues: 1233 helix: -0.03 (0.22), residues: 565 sheet: -0.41 (0.43), residues: 133 loop : -1.19 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1071 TYR 0.010 0.001 TYR E 338 PHE 0.014 0.001 PHE E 600 TRP 0.024 0.001 TRP E 612 HIS 0.004 0.001 HIS E 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10276) covalent geometry : angle 0.55289 / 0.28 (13914) hydrogen bonds : bond 0.03893 / 2.55 ( 415) hydrogen bonds : angle 4.02965 / 2.86 ( 1215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: D 956 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6170 (mp10) REVERT: D 960 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5943 (tt0) REVERT: D 962 GLU cc_start: 0.5826 (tm-30) cc_final: 0.5552 (tp30) REVERT: D 967 MET cc_start: 0.5450 (tmt) cc_final: 0.5210 (tpp) REVERT: E 226 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: E 233 ARG cc_start: 0.8318 (tmm-80) cc_final: 0.7907 (ttp-170) REVERT: E 265 GLU cc_start: 0.8404 (tp30) cc_final: 0.8179 (tt0) REVERT: E 434 ASP cc_start: 0.7525 (m-30) cc_final: 0.6971 (t0) REVERT: E 536 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8792 (tp) REVERT: E 682 ARG cc_start: 0.8452 (mtm-85) cc_final: 0.8240 (mtp180) REVERT: F 12 THR cc_start: 0.8926 (m) cc_final: 0.8679 (m) REVERT: F 56 LYS cc_start: 0.8648 (mttm) cc_final: 0.8313 (mttt) REVERT: F 76 LYS cc_start: 0.8585 (tttm) cc_final: 0.8190 (ttmp) REVERT: F 128 ASP cc_start: 0.8408 (t0) cc_final: 0.8122 (t0) REVERT: H 71 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7992 (tm-30) REVERT: I 24 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8317 (ttpp) REVERT: I 76 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: I 94 ASP cc_start: 0.8253 (t70) cc_final: 0.7964 (t70) REVERT: I 101 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: I 119 ARG cc_start: 0.8073 (ptt-90) cc_final: 0.7708 (ptm160) REVERT: J 199 ASP cc_start: 0.8154 (m-30) cc_final: 0.7675 (m-30) outliers start: 50 outliers final: 14 residues processed: 241 average time/residue: 0.6052 time to fit residues: 155.6174 Evaluate side-chains 225 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 956 GLN Chi-restraints excluded: chain D residue 960 GLU Chi-restraints excluded: chain D residue 965 ILE Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 759 ILE Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain L residue 60 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 0.0370 chunk 11 optimal weight: 9.9990 chunk 89 optimal weight: 0.0060 chunk 78 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 0.0070 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 0.8094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 232 HIS ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN E 327 ASN E 758 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 210 ASN L 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.146107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120581 restraints weight = 12665.725| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.96 r_work: 0.3369 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10276 Z= 0.122 Angle : 0.542 10.043 13914 Z= 0.275 Chirality : 0.041 0.146 1551 Planarity : 0.004 0.055 1802 Dihedral : 5.386 74.803 1374 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 4.41 % Allowed : 20.27 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.49 (0.24), residues: 1233 helix: 0.40 (0.23), residues: 564 sheet: -0.21 (0.43), residues: 124 loop : -1.06 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1071 TYR 0.012 0.001 TYR E 338 PHE 0.021 0.001 PHE F 106 TRP 0.021 0.001 TRP E 612 HIS 0.008 0.001 HIS E 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10276) covalent geometry : angle 0.54231 / 0.28 (13914) hydrogen bonds : bond 0.03629 / 2.39 ( 415) hydrogen bonds : angle 3.86707 / 2.74 ( 1215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 840 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7321 (ptp) REVERT: D 956 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.5973 (mp10) REVERT: D 967 MET cc_start: 0.5556 (tmt) cc_final: 0.5237 (tpp) REVERT: E 226 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: E 233 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7719 (ttp-170) REVERT: E 265 GLU cc_start: 0.8439 (tp30) cc_final: 0.8125 (tt0) REVERT: E 434 ASP cc_start: 0.7500 (m-30) cc_final: 0.6888 (t0) REVERT: E 446 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: E 555 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7170 (mtp-110) REVERT: F 12 THR cc_start: 0.8882 (m) cc_final: 0.8636 (m) REVERT: F 76 LYS cc_start: 0.8459 (tttm) cc_final: 0.8009 (ttmp) REVERT: F 128 ASP cc_start: 0.8348 (t0) cc_final: 0.8043 (t0) REVERT: H 71 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: H 112 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7900 (ptpp) REVERT: I 24 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8206 (ttpp) REVERT: I 76 GLN cc_start: 0.8323 (tt0) cc_final: 0.7994 (tm-30) REVERT: I 94 ASP cc_start: 0.8187 (t70) cc_final: 0.7809 (t70) REVERT: I 101 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: I 119 ARG cc_start: 0.8046 (ptt-90) cc_final: 0.7635 (ptm160) REVERT: J 145 GLU cc_start: 0.7991 (tt0) cc_final: 0.7694 (tm-30) REVERT: J 175 LYS cc_start: 0.7502 (mttm) cc_final: 0.7271 (mttm) REVERT: J 199 ASP cc_start: 0.7975 (m-30) cc_final: 0.7494 (m-30) REVERT: L 61 LYS cc_start: 0.7434 (tmtt) cc_final: 0.7203 (tptt) REVERT: L 75 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8031 (mt0) outliers start: 49 outliers final: 15 residues processed: 227 average time/residue: 0.5873 time to fit residues: 142.6662 Evaluate side-chains 215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 840 MET Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 956 GLN Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 273 CYS Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain E residue 722 ASP Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 75 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 52 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 64.6622 > 50:) chunk 110 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 0.1980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 232 HIS E 276 GLN ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 210 ASN L 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.143448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117899 restraints weight = 12600.382| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.92 r_work: 0.3329 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10276 Z= 0.165 Angle : 0.574 9.722 13914 Z= 0.291 Chirality : 0.043 0.151 1551 Planarity : 0.004 0.054 1802 Dihedral : 4.770 35.012 1367 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 4.14 % Allowed : 20.54 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.39 (0.24), residues: 1233 helix: 0.54 (0.23), residues: 568 sheet: -0.39 (0.42), residues: 135 loop : -1.03 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1071 TYR 0.013 0.001 TYR E 338 PHE 0.015 0.001 PHE F 91 TRP 0.021 0.002 TRP E 612 HIS 0.008 0.001 HIS E 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (10276) covalent geometry : angle 0.57411 / 0.29 (13914) hydrogen bonds : bond 0.03824 / 2.53 ( 415) hydrogen bonds : angle 3.91373 / 2.77 ( 1215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6364 (pt0) REVERT: D 953 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6540 (mp) REVERT: D 956 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.6066 (mp10) REVERT: D 967 MET cc_start: 0.5548 (tmt) cc_final: 0.5232 (tpp) REVERT: E 226 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: E 233 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.8029 (ttm110) REVERT: E 265 GLU cc_start: 0.8462 (tp30) cc_final: 0.8144 (tt0) REVERT: E 434 ASP cc_start: 0.7550 (m-30) cc_final: 0.6913 (t0) REVERT: E 446 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: F 12 THR cc_start: 0.8860 (m) cc_final: 0.8617 (m) REVERT: F 76 LYS cc_start: 0.8455 (tttm) cc_final: 0.8013 (ttmp) REVERT: F 128 ASP cc_start: 0.8406 (t0) cc_final: 0.8096 (t0) REVERT: H 71 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: H 85 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8312 (mtm110) REVERT: H 105 ASP cc_start: 0.8188 (t70) cc_final: 0.7913 (t0) REVERT: H 112 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7889 (ptpp) REVERT: I 24 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8187 (ttpp) REVERT: I 34 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7631 (mtm180) REVERT: I 94 ASP cc_start: 0.8243 (t70) cc_final: 0.7908 (t70) REVERT: I 101 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: I 119 ARG cc_start: 0.8062 (ptt-90) cc_final: 0.7664 (ptm160) REVERT: J 145 GLU cc_start: 0.7958 (tt0) cc_final: 0.7635 (tm-30) REVERT: J 175 LYS cc_start: 0.7461 (mttm) cc_final: 0.7258 (mttm) REVERT: J 192 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6111 (mtmt) REVERT: J 199 ASP cc_start: 0.8006 (m-30) cc_final: 0.7524 (m-30) REVERT: L 75 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8176 (mt0) outliers start: 46 outliers final: 19 residues processed: 223 average time/residue: 0.5796 time to fit residues: 138.6593 Evaluate side-chains 224 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 938 SER Chi-restraints excluded: chain D residue 952 GLN Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain D residue 956 GLN Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 722 ASP Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 104 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain J residue 198 GLU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 75 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 43 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 315 GLN E 327 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118762 restraints weight = 12641.946| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.95 r_work: 0.3358 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10276 Z= 0.114 Angle : 0.537 9.960 13914 Z= 0.271 Chirality : 0.041 0.144 1551 Planarity : 0.004 0.053 1802 Dihedral : 4.532 33.538 1367 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 3.96 % Allowed : 22.16 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1233 helix: 0.75 (0.23), residues: 569 sheet: -0.25 (0.42), residues: 127 loop : -0.97 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1071 TYR 0.013 0.001 TYR E 338 PHE 0.020 0.001 PHE F 106 TRP 0.018 0.001 TRP E 612 HIS 0.007 0.001 HIS E 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (10276) covalent geometry : angle 0.53696 / 0.27 (13914) hydrogen bonds : bond 0.03394 / 2.24 ( 415) hydrogen bonds : angle 3.75054 / 2.65 ( 1215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6203 (pt0) REVERT: D 953 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6370 (mp) REVERT: D 956 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.6074 (mp10) REVERT: D 967 MET cc_start: 0.5638 (tmt) cc_final: 0.5391 (tpp) REVERT: E 226 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: E 233 ARG cc_start: 0.8119 (tmm-80) cc_final: 0.7670 (ttm110) REVERT: E 265 GLU cc_start: 0.8429 (tp30) cc_final: 0.8086 (tt0) REVERT: E 434 ASP cc_start: 0.7377 (m-30) cc_final: 0.6762 (t0) REVERT: E 446 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: F 56 LYS cc_start: 0.8261 (mttm) cc_final: 0.7894 (mttt) REVERT: F 76 LYS cc_start: 0.8250 (tttm) cc_final: 0.7756 (ttmp) REVERT: F 103 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: F 128 ASP cc_start: 0.8312 (t0) cc_final: 0.8004 (t0) REVERT: H 71 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: H 105 ASP cc_start: 0.8134 (t70) cc_final: 0.7880 (t0) REVERT: H 112 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7775 (ptpp) REVERT: I 24 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8115 (ttpp) REVERT: I 94 ASP cc_start: 0.8172 (t70) cc_final: 0.7778 (t70) REVERT: I 101 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: I 119 ARG cc_start: 0.7974 (ptt-90) cc_final: 0.7525 (ptm160) REVERT: J 145 GLU cc_start: 0.7947 (tt0) cc_final: 0.7620 (tm-30) REVERT: J 192 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.5960 (mtmt) REVERT: J 199 ASP cc_start: 0.7765 (m-30) cc_final: 0.7303 (m-30) REVERT: L 61 LYS cc_start: 0.7263 (tmtt) cc_final: 0.7043 (tptt) outliers start: 44 outliers final: 18 residues processed: 223 average time/residue: 0.6039 time to fit residues: 143.8911 Evaluate side-chains 216 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 938 SER Chi-restraints excluded: chain D residue 952 GLN Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain D residue 956 GLN Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 273 CYS Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain J residue 198 GLU Chi-restraints excluded: chain L residue 60 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 232 HIS E 315 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119147 restraints weight = 12559.112| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.93 r_work: 0.3365 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10276 Z= 0.117 Angle : 0.541 10.038 13914 Z= 0.272 Chirality : 0.041 0.146 1551 Planarity : 0.004 0.053 1802 Dihedral : 4.470 33.024 1367 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 3.96 % Allowed : 22.79 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1233 helix: 0.94 (0.23), residues: 563 sheet: -0.46 (0.41), residues: 137 loop : -0.85 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1057 TYR 0.018 0.001 TYR E 314 PHE 0.012 0.001 PHE E 600 TRP 0.017 0.001 TRP E 612 HIS 0.008 0.001 HIS E 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10276) covalent geometry : angle 0.54097 / 0.27 (13914) hydrogen bonds : bond 0.03340 / 2.22 ( 415) hydrogen bonds : angle 3.71109 / 2.62 ( 1215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.6153 (pt0) REVERT: D 953 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6416 (mp) REVERT: D 956 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6007 (mp10) REVERT: D 967 MET cc_start: 0.5665 (tmt) cc_final: 0.5424 (tpp) REVERT: E 226 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: E 233 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7761 (ttm110) REVERT: E 265 GLU cc_start: 0.8424 (tp30) cc_final: 0.8091 (tt0) REVERT: E 349 LYS cc_start: 0.7846 (ttpt) cc_final: 0.6811 (tptp) REVERT: E 434 ASP cc_start: 0.7410 (m-30) cc_final: 0.6824 (t0) REVERT: E 446 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: E 534 SER cc_start: 0.8075 (m) cc_final: 0.7454 (p) REVERT: E 708 LYS cc_start: 0.7930 (pttm) cc_final: 0.7715 (mtmm) REVERT: F 56 LYS cc_start: 0.8260 (mttm) cc_final: 0.7901 (mttt) REVERT: F 76 LYS cc_start: 0.8257 (tttm) cc_final: 0.7785 (ttmp) REVERT: F 103 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: F 128 ASP cc_start: 0.8316 (t0) cc_final: 0.8033 (t0) REVERT: H 71 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: H 85 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8121 (mtm110) REVERT: H 105 ASP cc_start: 0.8125 (t70) cc_final: 0.7837 (t0) REVERT: H 112 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7749 (ptpp) REVERT: I 24 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8150 (ttpp) REVERT: I 94 ASP cc_start: 0.8179 (t70) cc_final: 0.7815 (t70) REVERT: I 101 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: I 119 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7616 (ptm160) REVERT: J 145 GLU cc_start: 0.7903 (tt0) cc_final: 0.7599 (tm-30) REVERT: J 192 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.5955 (mtmt) REVERT: J 199 ASP cc_start: 0.7722 (m-30) cc_final: 0.7278 (m-30) outliers start: 44 outliers final: 19 residues processed: 228 average time/residue: 0.5999 time to fit residues: 146.5025 Evaluate side-chains 223 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 938 SER Chi-restraints excluded: chain D residue 952 GLN Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain D residue 956 GLN Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 273 CYS Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain E residue 593 PHE Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain J residue 198 GLU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 114 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 315 GLN E 327 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.143856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118778 restraints weight = 12597.072| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.94 r_work: 0.3358 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10276 Z= 0.125 Angle : 0.545 10.095 13914 Z= 0.274 Chirality : 0.041 0.145 1551 Planarity : 0.004 0.053 1802 Dihedral : 4.461 33.407 1367 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 3.96 % Allowed : 23.42 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1233 helix: 1.07 (0.23), residues: 563 sheet: -0.52 (0.40), residues: 137 loop : -0.80 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1057 TYR 0.015 0.001 TYR E 338 PHE 0.017 0.001 PHE F 106 TRP 0.016 0.001 TRP E 612 HIS 0.005 0.001 HIS E 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (10276) covalent geometry : angle 0.54525 / 0.27 (13914) hydrogen bonds : bond 0.03333 / 2.22 ( 415) hydrogen bonds : angle 3.72320 / 2.63 ( 1215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6170 (pt0) REVERT: D 953 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6422 (mp) REVERT: D 956 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6019 (mp10) REVERT: D 967 MET cc_start: 0.5623 (tmt) cc_final: 0.5386 (tpp) REVERT: E 226 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: E 233 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7792 (ttm110) REVERT: E 265 GLU cc_start: 0.8404 (tp30) cc_final: 0.8067 (tt0) REVERT: E 349 LYS cc_start: 0.7861 (ttpt) cc_final: 0.6868 (tptp) REVERT: E 434 ASP cc_start: 0.7368 (m-30) cc_final: 0.6822 (t0) REVERT: E 446 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7181 (mm-30) REVERT: E 534 SER cc_start: 0.8042 (m) cc_final: 0.7440 (p) REVERT: E 708 LYS cc_start: 0.7911 (pttm) cc_final: 0.7704 (mtmm) REVERT: F 56 LYS cc_start: 0.8221 (mttm) cc_final: 0.7852 (mttt) REVERT: F 63 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7407 (ptt90) REVERT: F 76 LYS cc_start: 0.8249 (tttm) cc_final: 0.7784 (ttmp) REVERT: F 103 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7292 (mm-30) REVERT: F 128 ASP cc_start: 0.8314 (t0) cc_final: 0.8000 (t0) REVERT: H 71 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: H 85 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8062 (mtm110) REVERT: H 105 ASP cc_start: 0.8105 (t70) cc_final: 0.7818 (t0) REVERT: H 112 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7732 (ptpp) REVERT: H 124 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7564 (p) REVERT: I 24 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8165 (ttpp) REVERT: I 94 ASP cc_start: 0.8109 (t70) cc_final: 0.7770 (t70) REVERT: I 101 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: I 119 ARG cc_start: 0.8022 (ptt-90) cc_final: 0.7589 (ptm160) REVERT: J 145 GLU cc_start: 0.7880 (tt0) cc_final: 0.7595 (tm-30) REVERT: J 192 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6041 (mtmt) outliers start: 44 outliers final: 20 residues processed: 220 average time/residue: 0.6042 time to fit residues: 142.2731 Evaluate side-chains 225 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 938 SER Chi-restraints excluded: chain D residue 952 GLN Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain D residue 956 GLN Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 273 CYS Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain E residue 593 PHE Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain J residue 198 GLU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 114 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 315 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118949 restraints weight = 12558.947| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.95 r_work: 0.3362 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10276 Z= 0.120 Angle : 0.545 10.247 13914 Z= 0.274 Chirality : 0.041 0.147 1551 Planarity : 0.004 0.053 1802 Dihedral : 4.405 33.024 1367 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer: Outliers : 3.15 % Allowed : 24.50 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1233 helix: 1.13 (0.23), residues: 566 sheet: -0.50 (0.40), residues: 137 loop : -0.71 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1057 TYR 0.010 0.001 TYR I 120 PHE 0.012 0.001 PHE E 600 TRP 0.014 0.001 TRP E 612 HIS 0.007 0.001 HIS E 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10276) covalent geometry : angle 0.54494 / 0.27 (13914) hydrogen bonds : bond 0.03289 / 2.19 ( 415) hydrogen bonds : angle 3.75522 / 2.63 ( 1215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6174 (tt0) REVERT: D 953 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6464 (mp) REVERT: D 956 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.5903 (mp10) REVERT: D 967 MET cc_start: 0.5612 (tmt) cc_final: 0.5386 (tpp) REVERT: E 226 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: E 233 ARG cc_start: 0.8164 (tmm-80) cc_final: 0.7726 (ttm110) REVERT: E 265 GLU cc_start: 0.8404 (tp30) cc_final: 0.8081 (tt0) REVERT: E 349 LYS cc_start: 0.7843 (ttpt) cc_final: 0.6905 (tptt) REVERT: E 434 ASP cc_start: 0.7331 (m-30) cc_final: 0.6808 (t0) REVERT: E 442 MET cc_start: 0.8065 (ptp) cc_final: 0.7338 (ptt) REVERT: E 446 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: E 534 SER cc_start: 0.7993 (m) cc_final: 0.7378 (p) REVERT: E 555 ARG cc_start: 0.7535 (mtm110) cc_final: 0.7237 (mtp-110) REVERT: E 708 LYS cc_start: 0.7891 (pttm) cc_final: 0.7669 (mtmm) REVERT: F 56 LYS cc_start: 0.8172 (mttm) cc_final: 0.7798 (mttt) REVERT: F 63 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7934 (ptt90) REVERT: F 64 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8457 (mt0) REVERT: F 76 LYS cc_start: 0.8223 (tttm) cc_final: 0.7769 (ttmp) REVERT: F 103 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: F 128 ASP cc_start: 0.8313 (t0) cc_final: 0.8000 (t0) REVERT: H 71 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: H 85 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8189 (mtm110) REVERT: H 105 ASP cc_start: 0.8155 (t70) cc_final: 0.7889 (t0) REVERT: H 112 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7713 (ptpp) REVERT: H 124 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7552 (p) REVERT: I 24 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8174 (ttpp) REVERT: I 94 ASP cc_start: 0.8093 (t70) cc_final: 0.7764 (t70) REVERT: I 101 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: I 119 ARG cc_start: 0.7996 (ptt-90) cc_final: 0.7580 (ptm160) REVERT: J 145 GLU cc_start: 0.7870 (tt0) cc_final: 0.7599 (tm-30) REVERT: J 192 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.5991 (mtmt) REVERT: L 104 ARG cc_start: 0.7287 (tpm170) cc_final: 0.7060 (tpm170) outliers start: 35 outliers final: 20 residues processed: 218 average time/residue: 0.5859 time to fit residues: 136.4939 Evaluate side-chains 226 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 938 SER Chi-restraints excluded: chain D residue 952 GLN Chi-restraints excluded: chain D residue 953 ILE Chi-restraints excluded: chain D residue 956 GLN Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 273 CYS Chi-restraints excluded: chain E residue 326 ASN Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain E residue 593 PHE Chi-restraints excluded: chain E residue 775 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 ARG Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain L residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 0.0050 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 315 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121306 restraints weight = 12523.112| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.99 r_work: 0.3376 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10276 Z= 0.103 Angle : 0.538 10.509 13914 Z= 0.270 Chirality : 0.040 0.143 1551 Planarity : 0.004 0.052 1802 Dihedral : 4.267 32.132 1367 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 2.25 % Allowed : 25.50 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.24), residues: 1233 helix: 1.23 (0.23), residues: 567 sheet: -0.24 (0.41), residues: 127 loop : -0.74 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1071 TYR 0.017 0.001 TYR E 338 PHE 0.017 0.001 PHE F 106 TRP 0.016 0.001 TRP E 612 HIS 0.005 0.001 HIS E 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (10276) covalent geometry : angle 0.53813 / 0.27 (13914) hydrogen bonds : bond 0.03060 / 2.06 ( 415) hydrogen bonds : angle 3.67070 / 2.58 ( 1215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6363 (tt0) REVERT: D 956 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6018 (mp10) REVERT: E 226 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: E 233 ARG cc_start: 0.8248 (tmm-80) cc_final: 0.7842 (ttm110) REVERT: E 265 GLU cc_start: 0.8460 (tp30) cc_final: 0.8143 (tt0) REVERT: E 349 LYS cc_start: 0.7908 (ttpt) cc_final: 0.6908 (tptp) REVERT: E 434 ASP cc_start: 0.7341 (m-30) cc_final: 0.6873 (t0) REVERT: E 442 MET cc_start: 0.8114 (ptp) cc_final: 0.7417 (ptt) REVERT: E 446 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7275 (mm-30) REVERT: E 534 SER cc_start: 0.7899 (m) cc_final: 0.7402 (p) REVERT: E 555 ARG cc_start: 0.7533 (mtm110) cc_final: 0.7224 (mtp-110) REVERT: F 56 LYS cc_start: 0.8234 (mttm) cc_final: 0.7868 (mttt) REVERT: F 76 LYS cc_start: 0.8291 (tttm) cc_final: 0.7893 (ttmm) REVERT: F 103 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: F 128 ASP cc_start: 0.8362 (t0) cc_final: 0.8085 (t0) REVERT: H 71 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: H 105 ASP cc_start: 0.8155 (t70) cc_final: 0.7896 (t0) REVERT: I 94 ASP cc_start: 0.8149 (t70) cc_final: 0.7850 (t70) REVERT: I 101 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: I 119 ARG cc_start: 0.8016 (ptt-90) cc_final: 0.7604 (ptm160) REVERT: J 176 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6880 (tpt) REVERT: L 104 ARG cc_start: 0.7358 (tpm170) cc_final: 0.7130 (tpm170) outliers start: 25 outliers final: 13 residues processed: 211 average time/residue: 0.5847 time to fit residues: 132.0143 Evaluate side-chains 214 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 952 GLN Chi-restraints excluded: chain D residue 956 GLN Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 273 CYS Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain L residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.0570 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.119486 restraints weight = 12634.284| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.03 r_work: 0.3374 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10276 Z= 0.116 Angle : 0.552 10.791 13914 Z= 0.274 Chirality : 0.041 0.147 1551 Planarity : 0.004 0.051 1802 Dihedral : 4.168 22.513 1365 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 2.25 % Allowed : 25.86 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1233 helix: 1.27 (0.23), residues: 567 sheet: -0.18 (0.41), residues: 127 loop : -0.72 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1057 TYR 0.016 0.001 TYR E 338 PHE 0.012 0.001 PHE E 600 TRP 0.016 0.001 TRP E 612 HIS 0.005 0.001 HIS E 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10276) covalent geometry : angle 0.55223 / 0.27 (13914) hydrogen bonds : bond 0.03161 / 2.12 ( 415) hydrogen bonds : angle 3.68569 / 2.58 ( 1215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4190.55 seconds wall clock time: 72 minutes 13.01 seconds (4333.01 seconds total)