Starting phenix.real_space_refine on Mon Jul 28 03:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7egg_31116/07_2025/7egg_31116.cif Found real_map, /net/cci-nas-00/data/ceres_data/7egg_31116/07_2025/7egg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7egg_31116/07_2025/7egg_31116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7egg_31116/07_2025/7egg_31116.map" model { file = "/net/cci-nas-00/data/ceres_data/7egg_31116/07_2025/7egg_31116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7egg_31116/07_2025/7egg_31116.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.100 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.75, per 1000 atoms: 0.67 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.10 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: 3.38 Time building geometry restraints manager: 3.02 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: 5.200 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.440 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 8.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.002 TRP E 612 HIS 0.005 0.001 HIS J 215 PHE 0.028 0.002 PHE E 600 TYR 0.037 0.002 TYR E 274 ARG 0.009 0.001 ARG E 787 Details of bonding type rmsd hydrogen bonds : bond 0.24607 ( 415) hydrogen bonds : angle 8.94623 ( 1215) covalent geometry : bond 0.00755 (10276) covalent geometry : angle 1.13125 (13914) *********************** 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 : 1.560 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: 1.8039 time to fit residues: 579.2468 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 : 2.059 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124703 restraints weight = 12536.605| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.86 r_work: 0.3416 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (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 TRP 0.030 0.002 TRP E 612 HIS 0.005 0.001 HIS L 119 PHE 0.014 0.001 PHE E 600 TYR 0.012 0.001 TYR E 274 ARG 0.007 0.001 ARG D1071 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 415) hydrogen bonds : angle 4.49273 ( 1215) covalent geometry : bond 0.00309 (10276) covalent geometry : angle 0.59266 (13914) *********************** 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 : 1.245 Fit side-chains revert: symmetry clash REVERT: D 960 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.6076 (tm-30) REVERT: D 967 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.5150 (tpp) REVERT: E 226 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: E 265 GLU cc_start: 0.8437 (tp30) cc_final: 0.8231 (tt0) REVERT: E 434 ASP cc_start: 0.7617 (m-30) cc_final: 0.6951 (t0) REVERT: E 536 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8828 (tp) REVERT: F 56 LYS cc_start: 0.8725 (mttm) cc_final: 0.8331 (mttt) REVERT: F 76 LYS cc_start: 0.8610 (tttm) cc_final: 0.8294 (ttmm) REVERT: F 128 ASP cc_start: 0.8419 (t0) cc_final: 0.8046 (t70) REVERT: H 117 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6978 (mpt) REVERT: I 94 ASP cc_start: 0.8344 (t70) cc_final: 0.8060 (t70) REVERT: J 199 ASP cc_start: 0.8314 (m-30) cc_final: 0.7765 (m-30) REVERT: L 83 MET cc_start: 0.8517 (tpp) cc_final: 0.8203 (ttp) outliers start: 53 outliers final: 21 residues processed: 264 average time/residue: 1.6951 time to fit residues: 478.1963 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 : 1.143 ------------------------------------------------------------------------------- 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 82 optimal weight: 0.9980 chunk 80 optimal weight: 0.0030 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 856 ASN E 315 GLN E 618 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 = 0.3841 r_free = 0.3841 target = 0.151078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125927 restraints weight = 12669.941| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.87 r_work: 0.3443 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10276 Z= 0.107 Angle : 0.541 10.191 13914 Z= 0.277 Chirality : 0.041 0.142 1551 Planarity : 0.005 0.056 1802 Dihedral : 5.903 75.351 1380 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1233 helix: 0.00 (0.22), residues: 565 sheet: -0.43 (0.43), residues: 133 loop : -1.19 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 612 HIS 0.004 0.001 HIS L 119 PHE 0.013 0.001 PHE E 600 TYR 0.010 0.001 TYR E 338 ARG 0.007 0.000 ARG D1071 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 415) hydrogen bonds : angle 3.99075 ( 1215) covalent geometry : bond 0.00238 (10276) covalent geometry : angle 0.54070 (13914) *********************** 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 268 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: D 840 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7259 (ptp) REVERT: D 956 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6259 (mp10) REVERT: D 960 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.6008 (tt0) REVERT: D 962 GLU cc_start: 0.5801 (tm-30) cc_final: 0.5527 (tp30) REVERT: D 967 MET cc_start: 0.5450 (tmt) cc_final: 0.5226 (tpp) REVERT: E 226 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: E 233 ARG cc_start: 0.8343 (tmm-80) cc_final: 0.7939 (ttp-170) REVERT: E 425 ASN cc_start: 0.8636 (p0) cc_final: 0.8436 (p0) REVERT: E 434 ASP cc_start: 0.7577 (m-30) cc_final: 0.7040 (t0) REVERT: E 536 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8770 (tp) REVERT: F 12 THR cc_start: 0.8945 (m) cc_final: 0.8708 (m) REVERT: F 56 LYS cc_start: 0.8651 (mttm) cc_final: 0.8330 (mttt) REVERT: F 76 LYS cc_start: 0.8650 (tttm) cc_final: 0.8292 (ttmp) REVERT: F 128 ASP cc_start: 0.8425 (t0) cc_final: 0.8141 (t0) REVERT: H 71 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: I 24 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8372 (ttpp) REVERT: I 76 GLN cc_start: 0.8659 (tt0) cc_final: 0.8261 (tm-30) REVERT: I 94 ASP cc_start: 0.8332 (t70) cc_final: 0.8084 (t70) REVERT: I 119 ARG cc_start: 0.8063 (ptt-90) cc_final: 0.7733 (ptm160) REVERT: J 145 GLU cc_start: 0.7943 (tt0) cc_final: 0.7737 (tm-30) REVERT: J 199 ASP cc_start: 0.8152 (m-30) cc_final: 0.7700 (m-30) REVERT: L 61 LYS cc_start: 0.7659 (tmtt) cc_final: 0.7422 (tptt) outliers start: 50 outliers final: 14 residues processed: 243 average time/residue: 1.4182 time to fit residues: 367.7225 Evaluate side-chains 223 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 438 LEU 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 85 SER 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 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 HIS E 315 GLN E 327 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122251 restraints weight = 12579.987| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.95 r_work: 0.3405 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10276 Z= 0.107 Angle : 0.532 10.269 13914 Z= 0.269 Chirality : 0.040 0.144 1551 Planarity : 0.004 0.054 1802 Dihedral : 5.100 75.650 1372 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 4.05 % Allowed : 21.17 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.24), residues: 1233 helix: 0.47 (0.23), residues: 564 sheet: -0.18 (0.43), residues: 124 loop : -1.03 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 612 HIS 0.008 0.001 HIS E 605 PHE 0.022 0.001 PHE F 106 TYR 0.013 0.001 TYR E 338 ARG 0.006 0.000 ARG D1071 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 415) hydrogen bonds : angle 3.79459 ( 1215) covalent geometry : bond 0.00245 (10276) covalent geometry : angle 0.53159 (13914) *********************** 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 252 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: D 840 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7219 (ptp) REVERT: D 956 GLN cc_start: 0.6293 (OUTLIER) cc_final: 0.5949 (mp10) REVERT: D 967 MET cc_start: 0.5588 (tmt) cc_final: 0.5292 (tpp) REVERT: E 226 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: E 233 ARG cc_start: 0.8147 (tmm-80) cc_final: 0.7637 (ttp-170) REVERT: E 298 LEU cc_start: 0.8666 (mt) cc_final: 0.8451 (mt) REVERT: E 341 ILE cc_start: 0.8388 (mt) cc_final: 0.8130 (mm) REVERT: E 425 ASN cc_start: 0.8560 (p0) cc_final: 0.8304 (p0) REVERT: E 434 ASP cc_start: 0.7477 (m-30) cc_final: 0.6843 (t0) REVERT: E 446 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: E 536 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8760 (tp) REVERT: E 708 LYS cc_start: 0.7918 (pttm) cc_final: 0.7701 (mtmm) REVERT: F 12 THR cc_start: 0.8858 (m) cc_final: 0.8615 (m) REVERT: F 76 LYS cc_start: 0.8413 (tttm) cc_final: 0.7961 (ttmp) REVERT: F 84 TYR cc_start: 0.8078 (m-80) cc_final: 0.7862 (m-80) REVERT: F 128 ASP cc_start: 0.8335 (t0) cc_final: 0.8048 (t0) REVERT: H 71 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: I 24 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8171 (ttpp) REVERT: I 94 ASP cc_start: 0.8228 (t70) cc_final: 0.7836 (t70) REVERT: I 119 ARG cc_start: 0.8042 (ptt-90) cc_final: 0.7600 (ptm160) REVERT: J 145 GLU cc_start: 0.7991 (tt0) cc_final: 0.7654 (tm-30) REVERT: J 199 ASP cc_start: 0.7895 (m-30) cc_final: 0.7416 (m-30) outliers start: 45 outliers final: 13 residues processed: 230 average time/residue: 1.3454 time to fit residues: 331.1655 Evaluate side-chains 220 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 273 CYS Chi-restraints excluded: chain E residue 369 LYS Chi-restraints excluded: chain E residue 446 GLU 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 50 ILE 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 85 SER Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain L residue 60 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 12 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 911 GLN E 232 HIS E 276 GLN E 315 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122497 restraints weight = 12570.735| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.96 r_work: 0.3402 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10276 Z= 0.107 Angle : 0.531 10.339 13914 Z= 0.267 Chirality : 0.040 0.144 1551 Planarity : 0.004 0.052 1802 Dihedral : 4.407 31.361 1367 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 2.97 % Allowed : 22.43 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1233 helix: 0.70 (0.23), residues: 567 sheet: -0.29 (0.42), residues: 127 loop : -1.00 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 612 HIS 0.008 0.001 HIS E 605 PHE 0.012 0.001 PHE E 600 TYR 0.014 0.001 TYR E 338 ARG 0.005 0.000 ARG D1071 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 415) hydrogen bonds : angle 3.71496 ( 1215) covalent geometry : bond 0.00246 (10276) covalent geometry : angle 0.53087 (13914) *********************** 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 232 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: D 840 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7216 (ptp) REVERT: D 952 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6225 (pt0) REVERT: D 956 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.5980 (mp10) REVERT: D 967 MET cc_start: 0.5635 (tmt) cc_final: 0.5346 (tpp) REVERT: E 213 MET cc_start: 0.7183 (mmm) cc_final: 0.6935 (mmm) REVERT: E 226 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: E 233 ARG cc_start: 0.8200 (tmm-80) cc_final: 0.7744 (ttm110) REVERT: E 298 LEU cc_start: 0.8646 (mt) cc_final: 0.8421 (mt) REVERT: E 341 ILE cc_start: 0.8385 (mt) cc_final: 0.8134 (mm) REVERT: E 425 ASN cc_start: 0.8535 (p0) cc_final: 0.8279 (p0) REVERT: E 434 ASP cc_start: 0.7425 (m-30) cc_final: 0.6838 (t0) REVERT: E 446 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7210 (mm-30) REVERT: E 536 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8766 (tp) REVERT: F 12 THR cc_start: 0.8848 (m) cc_final: 0.8603 (m) REVERT: F 56 LYS cc_start: 0.8296 (mttm) cc_final: 0.7943 (mttt) REVERT: F 76 LYS cc_start: 0.8373 (tttm) cc_final: 0.7951 (ttmp) REVERT: F 128 ASP cc_start: 0.8319 (t0) cc_final: 0.8043 (t0) REVERT: H 71 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: I 24 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8180 (ttpp) REVERT: I 94 ASP cc_start: 0.8136 (t70) cc_final: 0.7790 (t70) REVERT: I 119 ARG cc_start: 0.8015 (ptt-90) cc_final: 0.7547 (ptm160) REVERT: J 145 GLU cc_start: 0.7906 (tt0) cc_final: 0.7649 (tm-30) REVERT: J 199 ASP cc_start: 0.7768 (m-30) cc_final: 0.7317 (m-30) REVERT: L 61 LYS cc_start: 0.7359 (tmtt) cc_final: 0.7126 (tptt) REVERT: L 75 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8087 (mt0) outliers start: 33 outliers final: 14 residues processed: 213 average time/residue: 1.3033 time to fit residues: 297.3414 Evaluate side-chains 211 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 952 GLN Chi-restraints excluded: chain D residue 956 GLN 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 446 GLU Chi-restraints excluded: chain E residue 536 LEU 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 J residue 127 THR 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 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118560 restraints weight = 12516.780| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.93 r_work: 0.3362 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3346 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= 0.130 Angle : 0.546 10.114 13914 Z= 0.274 Chirality : 0.041 0.149 1551 Planarity : 0.004 0.052 1802 Dihedral : 4.451 32.463 1367 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 4.32 % Allowed : 21.53 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.24), residues: 1233 helix: 0.82 (0.23), residues: 565 sheet: -0.24 (0.42), residues: 127 loop : -0.96 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 612 HIS 0.006 0.001 HIS E 605 PHE 0.019 0.001 PHE F 106 TYR 0.014 0.001 TYR E 338 ARG 0.004 0.000 ARG D1071 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 415) hydrogen bonds : angle 3.73214 ( 1215) covalent geometry : bond 0.00307 (10276) covalent geometry : angle 0.54580 (13914) *********************** 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 240 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: D 840 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7306 (ptp) REVERT: D 952 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6179 (pt0) REVERT: D 956 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.5986 (mp10) REVERT: D 967 MET cc_start: 0.5677 (tmt) cc_final: 0.5395 (tpp) REVERT: E 226 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: E 233 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7783 (ttm110) REVERT: E 341 ILE cc_start: 0.8439 (mt) cc_final: 0.8170 (mm) REVERT: E 425 ASN cc_start: 0.8563 (p0) cc_final: 0.8300 (p0) REVERT: E 434 ASP cc_start: 0.7411 (m-30) cc_final: 0.6772 (t0) REVERT: E 446 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: F 12 THR cc_start: 0.8854 (m) cc_final: 0.8626 (m) REVERT: F 56 LYS cc_start: 0.8231 (mttm) cc_final: 0.7886 (mttt) REVERT: F 76 LYS cc_start: 0.8256 (tttm) cc_final: 0.7772 (ttmp) REVERT: F 84 TYR cc_start: 0.8109 (m-80) cc_final: 0.7908 (m-80) REVERT: F 128 ASP cc_start: 0.8317 (t0) cc_final: 0.8020 (t0) REVERT: H 71 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: H 105 ASP cc_start: 0.8099 (t70) cc_final: 0.7816 (t0) REVERT: I 76 GLN cc_start: 0.8414 (tt0) cc_final: 0.8195 (tm-30) REVERT: I 94 ASP cc_start: 0.8170 (t70) cc_final: 0.7794 (t70) REVERT: I 101 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7763 (mt0) REVERT: I 119 ARG cc_start: 0.7967 (ptt-90) cc_final: 0.7487 (ptm160) REVERT: J 192 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6091 (mtmt) outliers start: 48 outliers final: 22 residues processed: 217 average time/residue: 1.4521 time to fit residues: 337.9273 Evaluate side-chains 221 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 840 MET 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 956 GLN Chi-restraints excluded: chain D residue 1074 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 229 LEU 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 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 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 58 LEU 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 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 HIS E 315 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS L 73 ASN L 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120321 restraints weight = 12689.190| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.95 r_work: 0.3386 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10276 Z= 0.107 Angle : 0.530 10.270 13914 Z= 0.265 Chirality : 0.040 0.145 1551 Planarity : 0.004 0.052 1802 Dihedral : 4.309 31.535 1367 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 3.60 % Allowed : 22.88 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1233 helix: 0.99 (0.23), residues: 564 sheet: -0.27 (0.42), residues: 127 loop : -0.87 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 612 HIS 0.005 0.001 HIS E 605 PHE 0.012 0.001 PHE E 600 TYR 0.015 0.001 TYR E 338 ARG 0.004 0.000 ARG D1071 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 415) hydrogen bonds : angle 3.65041 ( 1215) covalent geometry : bond 0.00246 (10276) covalent geometry : angle 0.53049 (13914) *********************** 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 231 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.6094 (tt0) REVERT: D 956 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.5915 (mp10) REVERT: D 967 MET cc_start: 0.5650 (tmt) cc_final: 0.5426 (tpp) REVERT: E 226 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: E 233 ARG cc_start: 0.8201 (tmm-80) cc_final: 0.7753 (ttm110) REVERT: E 341 ILE cc_start: 0.8422 (mt) cc_final: 0.8167 (mm) REVERT: E 425 ASN cc_start: 0.8527 (p0) cc_final: 0.8254 (p0) REVERT: E 434 ASP cc_start: 0.7358 (m-30) cc_final: 0.6842 (t0) REVERT: E 446 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: F 56 LYS cc_start: 0.8193 (mttm) cc_final: 0.7841 (mttt) REVERT: F 76 LYS cc_start: 0.8247 (tttm) cc_final: 0.7756 (ttmp) REVERT: F 103 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7276 (mm-30) REVERT: F 128 ASP cc_start: 0.8293 (t0) cc_final: 0.7989 (t0) REVERT: H 71 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7761 (tm-30) REVERT: H 85 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8054 (mtm110) REVERT: H 105 ASP cc_start: 0.8080 (t70) cc_final: 0.7835 (t0) REVERT: I 76 GLN cc_start: 0.8301 (tt0) cc_final: 0.8067 (tm-30) REVERT: I 94 ASP cc_start: 0.8105 (t70) cc_final: 0.7746 (t70) REVERT: I 119 ARG cc_start: 0.8000 (ptt-90) cc_final: 0.7536 (ptm160) REVERT: J 145 GLU cc_start: 0.7884 (tt0) cc_final: 0.7625 (tm-30) REVERT: J 192 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6028 (mtmt) outliers start: 40 outliers final: 17 residues processed: 215 average time/residue: 1.6682 time to fit residues: 383.3879 Evaluate side-chains 214 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 956 GLN 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 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 85 SER Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 176 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 75 optimal weight: 0.0020 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3758 r_free = 0.3758 target = 0.145805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119965 restraints weight = 12646.872| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.03 r_work: 0.3377 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3558 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= 0.108 Angle : 0.537 10.386 13914 Z= 0.266 Chirality : 0.041 0.153 1551 Planarity : 0.004 0.051 1802 Dihedral : 4.258 32.933 1367 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 3.42 % Allowed : 23.51 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1233 helix: 1.16 (0.23), residues: 564 sheet: -0.21 (0.41), residues: 127 loop : -0.86 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 612 HIS 0.007 0.001 HIS E 605 PHE 0.019 0.001 PHE F 106 TYR 0.014 0.001 TYR E 338 ARG 0.004 0.000 ARG D1057 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 415) hydrogen bonds : angle 3.62409 ( 1215) covalent geometry : bond 0.00253 (10276) covalent geometry : angle 0.53687 (13914) *********************** 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 234 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.6082 (tt0) REVERT: D 956 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.5871 (mp10) REVERT: D 967 MET cc_start: 0.5599 (tmt) cc_final: 0.5376 (tpp) REVERT: E 226 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: E 233 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7812 (ttm110) REVERT: E 341 ILE cc_start: 0.8445 (mt) cc_final: 0.8192 (mm) REVERT: E 349 LYS cc_start: 0.7939 (ttpt) cc_final: 0.6956 (tptp) REVERT: E 425 ASN cc_start: 0.8489 (p0) cc_final: 0.8202 (p0) REVERT: E 434 ASP cc_start: 0.7427 (m-30) cc_final: 0.6890 (t0) REVERT: E 446 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: F 56 LYS cc_start: 0.8200 (mttm) cc_final: 0.7818 (mttt) REVERT: F 76 LYS cc_start: 0.8265 (tttm) cc_final: 0.7803 (ttmp) REVERT: F 103 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: F 128 ASP cc_start: 0.8356 (t0) cc_final: 0.8068 (t0) REVERT: H 71 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: H 85 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8119 (mtm110) REVERT: H 105 ASP cc_start: 0.8149 (t70) cc_final: 0.7859 (t0) REVERT: I 94 ASP cc_start: 0.8173 (t70) cc_final: 0.7852 (t70) REVERT: I 119 ARG cc_start: 0.8020 (ptt-90) cc_final: 0.7565 (ptm160) REVERT: J 145 GLU cc_start: 0.7872 (tt0) cc_final: 0.7657 (tm-30) REVERT: J 192 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6119 (mtmt) outliers start: 38 outliers final: 20 residues processed: 218 average time/residue: 1.2829 time to fit residues: 299.5411 Evaluate side-chains 214 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 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 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 85 SER 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 198 GLU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain L residue 60 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 6.9990 chunk 60 optimal weight: 0.0370 chunk 114 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 82 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 0.0270 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 HIS E 315 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 119 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122831 restraints weight = 12719.503| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.01 r_work: 0.3418 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10276 Z= 0.096 Angle : 0.531 10.870 13914 Z= 0.262 Chirality : 0.040 0.145 1551 Planarity : 0.004 0.051 1802 Dihedral : 4.116 33.137 1367 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 2.43 % Allowed : 24.77 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1233 helix: 1.30 (0.23), residues: 564 sheet: -0.27 (0.41), residues: 129 loop : -0.85 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 612 HIS 0.005 0.001 HIS E 605 PHE 0.012 0.001 PHE E 600 TYR 0.016 0.001 TYR E 338 ARG 0.004 0.000 ARG D1071 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 415) hydrogen bonds : angle 3.54256 ( 1215) covalent geometry : bond 0.00218 (10276) covalent geometry : angle 0.53076 (13914) *********************** 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 228 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: D 952 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.5997 (tt0) REVERT: D 956 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.5888 (mp10) REVERT: E 226 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: E 233 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7833 (ttm110) REVERT: E 349 LYS cc_start: 0.7894 (ttpt) cc_final: 0.6977 (tptt) REVERT: E 425 ASN cc_start: 0.8435 (p0) cc_final: 0.8152 (p0) REVERT: E 434 ASP cc_start: 0.7388 (m-30) cc_final: 0.6905 (t0) REVERT: E 442 MET cc_start: 0.8099 (ptp) cc_final: 0.7384 (ptt) REVERT: E 446 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: E 525 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8131 (mm-30) REVERT: E 534 SER cc_start: 0.7908 (m) cc_final: 0.7397 (p) REVERT: E 593 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.9104 (m-80) REVERT: F 56 LYS cc_start: 0.8143 (mttm) cc_final: 0.7782 (mttt) REVERT: F 76 LYS cc_start: 0.8250 (tttm) cc_final: 0.7788 (ttmp) REVERT: F 128 ASP cc_start: 0.8343 (t0) cc_final: 0.8078 (t0) REVERT: H 71 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: H 105 ASP cc_start: 0.8141 (t70) cc_final: 0.7862 (t0) REVERT: I 94 ASP cc_start: 0.8129 (t70) cc_final: 0.7823 (t70) REVERT: I 119 ARG cc_start: 0.7978 (ptt-90) cc_final: 0.7478 (ptm160) REVERT: J 176 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6805 (tpp) REVERT: J 192 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6097 (mtmt) outliers start: 27 outliers final: 12 residues processed: 212 average time/residue: 1.3350 time to fit residues: 302.7602 Evaluate side-chains 211 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 435 SER Chi-restraints excluded: chain E residue 446 GLU Chi-restraints excluded: chain E residue 593 PHE Chi-restraints excluded: chain F residue 50 ILE 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 I residue 85 SER Chi-restraints excluded: chain J residue 127 THR Chi-restraints excluded: chain J residue 176 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 23 optimal weight: 0.0870 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 315 GLN E 618 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119569 restraints weight = 12596.049| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.95 r_work: 0.3380 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3693 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= 0.124 Angle : 0.569 11.154 13914 Z= 0.278 Chirality : 0.041 0.148 1551 Planarity : 0.004 0.051 1802 Dihedral : 4.242 34.011 1367 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 2.25 % Allowed : 25.32 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1233 helix: 1.24 (0.23), residues: 567 sheet: -0.26 (0.41), residues: 129 loop : -0.77 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 612 HIS 0.005 0.001 HIS E 605 PHE 0.017 0.001 PHE F 106 TYR 0.016 0.001 TYR E 338 ARG 0.004 0.000 ARG D1057 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 415) hydrogen bonds : angle 3.68540 ( 1215) covalent geometry : bond 0.00295 (10276) covalent geometry : angle 0.56900 (13914) ********************** 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 221 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: D 948 GLU cc_start: 0.7453 (tt0) cc_final: 0.6749 (mt-10) REVERT: D 952 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6116 (tt0) REVERT: D 956 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.5868 (mp10) REVERT: E 226 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: E 233 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7846 (ttm110) REVERT: E 425 ASN cc_start: 0.8509 (p0) cc_final: 0.8247 (p0) REVERT: E 434 ASP cc_start: 0.7463 (m-30) cc_final: 0.6960 (t0) REVERT: E 446 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: E 525 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8096 (mm-30) REVERT: E 731 MET cc_start: 0.8335 (mmt) cc_final: 0.8001 (mmt) REVERT: F 56 LYS cc_start: 0.8196 (mttm) cc_final: 0.7836 (mttt) REVERT: F 76 LYS cc_start: 0.8303 (tttm) cc_final: 0.7849 (ttmp) REVERT: F 128 ASP cc_start: 0.8346 (t0) cc_final: 0.8046 (t0) REVERT: H 71 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: H 105 ASP cc_start: 0.8104 (t70) cc_final: 0.7849 (t0) REVERT: I 119 ARG cc_start: 0.7988 (ptt-90) cc_final: 0.7508 (ptm160) REVERT: J 176 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6896 (tpp) REVERT: J 192 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6020 (mtmt) REVERT: L 112 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7157 (mp0) outliers start: 25 outliers final: 13 residues processed: 207 average time/residue: 1.2871 time to fit residues: 285.2501 Evaluate side-chains 213 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 233 ARG Chi-restraints excluded: chain E residue 273 CYS Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain E residue 446 GLU 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 I residue 85 SER 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 198 GLU 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: 2.9990 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3749 r_free = 0.3749 target = 0.144566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118464 restraints weight = 12593.069| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.01 r_work: 0.3371 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10276 Z= 0.123 Angle : 0.558 11.304 13914 Z= 0.275 Chirality : 0.041 0.148 1551 Planarity : 0.004 0.051 1802 Dihedral : 4.266 34.409 1367 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer: Outliers : 2.43 % Allowed : 25.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1233 helix: 1.27 (0.23), residues: 567 sheet: -0.11 (0.41), residues: 127 loop : -0.77 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 612 HIS 0.004 0.001 HIS E 605 PHE 0.013 0.001 PHE E 600 TYR 0.017 0.001 TYR E 338 ARG 0.004 0.000 ARG D1057 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 415) hydrogen bonds : angle 3.70294 ( 1215) covalent geometry : bond 0.00293 (10276) covalent geometry : angle 0.55789 (13914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9540.44 seconds wall clock time: 168 minutes 2.13 seconds (10082.13 seconds total)