Starting phenix.real_space_refine on Sat Jun 14 07:31:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo2_61641/06_2025/9jo2_61641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo2_61641/06_2025/9jo2_61641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jo2_61641/06_2025/9jo2_61641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo2_61641/06_2025/9jo2_61641.map" model { file = "/net/cci-nas-00/data/ceres_data/9jo2_61641/06_2025/9jo2_61641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo2_61641/06_2025/9jo2_61641.cif" } resolution = 3.0 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= 0.011 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: 6 Type Number sf(0) Gaussians P 292 5.49 5 S 25 5.16 5 Cl 1 4.86 5 C 9339 2.51 5 N 2976 2.21 5 O 3592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16225 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4209 Classifications: {'peptide': 512} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 492} Chain breaks: 4 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.92, per 1000 atoms: 0.61 Number of scatterers: 16225 At special positions: 0 Unit cell: (97.425, 116.91, 156.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 25 16.00 P 292 15.00 O 3592 8.00 N 2976 7.00 C 9339 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: 4.36 Conformation dependent library (CDL) restraints added in 1.5 seconds 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 11 sheets defined 65.6% alpha, 3.6% beta 141 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 7.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.873A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.542A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.561A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.605A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.740A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.726A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.743A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.684A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.508A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.010A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.453A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.506A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.593A pdb=" N LEU G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.588A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.672A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.534A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.520A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 114 Processing helix chain 'K' and resid 116 through 119 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 138 removed outlier: 3.786A pdb=" N ARG K 134 " --> pdb=" O ASP K 130 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN K 135 " --> pdb=" O PRO K 131 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU K 137 " --> pdb=" O PHE K 133 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP K 138 " --> pdb=" O ARG K 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 130 through 138' Processing helix chain 'K' and resid 197 through 199 No H-bonds generated for 'chain 'K' and resid 197 through 199' Processing helix chain 'K' and resid 200 through 212 Processing helix chain 'K' and resid 227 through 243 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.512A pdb=" N TRP K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU K 261 " --> pdb=" O LEU K 257 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR K 268 " --> pdb=" O ILE K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 Processing helix chain 'K' and resid 309 through 314 removed outlier: 3.831A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 329 removed outlier: 3.601A pdb=" N ARG K 328 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 343 removed outlier: 3.595A pdb=" N PHE K 343 " --> pdb=" O VAL K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 371 removed outlier: 4.318A pdb=" N LEU K 363 " --> pdb=" O ASN K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 386 removed outlier: 3.557A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 406 removed outlier: 3.606A pdb=" N GLN K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR K 403 " --> pdb=" O LYS K 399 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU K 405 " --> pdb=" O LEU K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 469 through 478 removed outlier: 3.723A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 501 through 516 removed outlier: 3.885A pdb=" N GLN K 505 " --> pdb=" O ALA K 501 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 removed outlier: 3.825A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 601 through 614 removed outlier: 4.216A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 4.005A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 658 removed outlier: 3.554A pdb=" N SER K 657 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.136A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.942A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.065A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.333A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 298 through 302 removed outlier: 6.228A pdb=" N GLU K 319 " --> pdb=" O ASN K 347 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU K 349 " --> pdb=" O GLU K 319 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY K 217 " --> pdb=" O ARG K 348 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 428 through 431 removed outlier: 3.742A pdb=" N VAL K 627 " --> pdb=" O LEU K 429 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 7.71 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2996 1.33 - 1.45: 5242 1.45 - 1.57: 8251 1.57 - 1.69: 582 1.69 - 1.81: 43 Bond restraints: 17114 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.34e-02 5.57e+03 3.12e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.528 1.484 0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" CA SER K 420 " pdb=" C SER K 420 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.20e+01 bond pdb=" N GLU K 418 " pdb=" CA GLU K 418 " ideal model delta sigma weight residual 1.457 1.413 0.044 1.29e-02 6.01e+03 1.18e+01 bond pdb=" CA VAL K 417 " pdb=" C VAL K 417 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.27e-02 6.20e+03 1.06e+01 ... (remaining 17109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 24010 2.62 - 5.24: 316 5.24 - 7.87: 39 7.87 - 10.49: 4 10.49 - 13.11: 3 Bond angle restraints: 24372 Sorted by residual: angle pdb=" CG ARG D 30 " pdb=" CD ARG D 30 " pdb=" NE ARG D 30 " ideal model delta sigma weight residual 112.00 99.47 12.53 2.20e+00 2.07e-01 3.25e+01 angle pdb=" N VAL K 417 " pdb=" CA VAL K 417 " pdb=" C VAL K 417 " ideal model delta sigma weight residual 109.34 97.58 11.76 2.08e+00 2.31e-01 3.20e+01 angle pdb=" C PRO K 423 " pdb=" N LYS K 424 " pdb=" CA LYS K 424 " ideal model delta sigma weight residual 121.42 113.44 7.98 1.43e+00 4.89e-01 3.11e+01 angle pdb=" O ASP K 416 " pdb=" C ASP K 416 " pdb=" N VAL K 417 " ideal model delta sigma weight residual 122.07 127.77 -5.70 1.03e+00 9.43e-01 3.06e+01 angle pdb=" CA ASP K 416 " pdb=" C ASP K 416 " pdb=" N VAL K 417 " ideal model delta sigma weight residual 117.07 110.92 6.15 1.14e+00 7.69e-01 2.91e+01 ... (remaining 24367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 8061 35.57 - 71.14: 1461 71.14 - 106.70: 34 106.70 - 142.27: 1 142.27 - 177.84: 13 Dihedral angle restraints: 9570 sinusoidal: 5836 harmonic: 3734 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 -127.22 -52.78 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA PRO K 489 " pdb=" C PRO K 489 " pdb=" N PRO K 490 " pdb=" CA PRO K 490 " ideal model delta harmonic sigma weight residual 180.00 132.26 47.74 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA TYR K 545 " pdb=" C TYR K 545 " pdb=" N CYS K 546 " pdb=" CA CYS K 546 " ideal model delta harmonic sigma weight residual 180.00 148.56 31.44 0 5.00e+00 4.00e-02 3.95e+01 ... (remaining 9567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2325 0.062 - 0.125: 401 0.125 - 0.187: 39 0.187 - 0.249: 2 0.249 - 0.312: 2 Chirality restraints: 2769 Sorted by residual: chirality pdb=" CB ILE K 244 " pdb=" CA ILE K 244 " pdb=" CG1 ILE K 244 " pdb=" CG2 ILE K 244 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA VAL K 417 " pdb=" N VAL K 417 " pdb=" C VAL K 417 " pdb=" CB VAL K 417 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C3' DG I 40 " pdb=" C4' DG I 40 " pdb=" O3' DG I 40 " pdb=" C2' DG I 40 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 2766 not shown) Planarity restraints: 2079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " -0.070 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO K 490 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 263 " 0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" CD GLU K 263 " -0.074 2.00e-02 2.50e+03 pdb=" OE1 GLU K 263 " 0.026 2.00e-02 2.50e+03 pdb=" OE2 GLU K 263 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN K 406 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO K 407 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO K 407 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 407 " -0.035 5.00e-02 4.00e+02 ... (remaining 2076 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 141 2.57 - 3.15: 13515 3.15 - 3.74: 28573 3.74 - 4.32: 39522 4.32 - 4.90: 58010 Nonbonded interactions: 139761 Sorted by model distance: nonbonded pdb=" O GLU K 535 " pdb=" OH TYR K 545 " model vdw 1.990 3.040 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.100 3.040 nonbonded pdb=" O ILE E 119 " pdb=" OG SER F 47 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.101 3.040 nonbonded pdb=" OD1 ASP K 494 " pdb=" ND1 HIS K 496 " model vdw 2.113 3.120 ... (remaining 139756 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 44.880 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.010 0.082 17114 Z= 0.424 Angle : 0.842 13.109 24372 Z= 0.479 Chirality : 0.048 0.312 2769 Planarity : 0.005 0.108 2079 Dihedral : 27.127 177.840 7150 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.10 % Favored : 90.58 % Rotamer: Outliers : 0.18 % Allowed : 0.82 % Favored : 98.99 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.16 % 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: -0.79 (0.24), residues: 1253 helix: 0.65 (0.19), residues: 766 sheet: -2.24 (0.65), residues: 75 loop : -2.42 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP K 267 HIS 0.008 0.002 HIS A 39 PHE 0.024 0.002 PHE K 574 TYR 0.025 0.002 TYR K 320 ARG 0.019 0.001 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.09812 ( 925) hydrogen bonds : angle 4.68746 ( 2379) covalent geometry : bond 0.00952 (17114) covalent geometry : angle 0.84192 (24372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8977 (m) cc_final: 0.8767 (p) REVERT: B 59 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8438 (tttp) REVERT: B 79 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8093 (mtpm) REVERT: C 90 ASP cc_start: 0.8619 (t0) cc_final: 0.8304 (t0) REVERT: H 48 ASP cc_start: 0.8870 (p0) cc_final: 0.8230 (p0) REVERT: K 91 LEU cc_start: 0.9098 (mp) cc_final: 0.8784 (pt) REVERT: K 267 TRP cc_start: 0.8302 (m100) cc_final: 0.7568 (m100) REVERT: K 361 HIS cc_start: 0.6423 (t-90) cc_final: 0.5770 (t-170) REVERT: K 652 GLN cc_start: 0.8638 (mp10) cc_final: 0.7815 (mp10) outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 1.5874 time to fit residues: 426.9152 Evaluate side-chains 153 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 421 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 84 GLN F 93 GLN G 84 GLN G 104 GLN ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS K 361 HIS K 471 GLN K 526 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.094585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068035 restraints weight = 42446.741| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.05 r_work: 0.3078 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17114 Z= 0.183 Angle : 0.680 9.393 24372 Z= 0.381 Chirality : 0.040 0.200 2769 Planarity : 0.005 0.089 2079 Dihedral : 30.332 176.452 4599 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 1.83 % Allowed : 14.30 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1253 helix: 1.39 (0.19), residues: 770 sheet: -2.03 (0.70), residues: 71 loop : -2.09 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 364 HIS 0.008 0.001 HIS K 111 PHE 0.047 0.002 PHE K 109 TYR 0.017 0.001 TYR K 320 ARG 0.017 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 925) hydrogen bonds : angle 3.59190 ( 2379) covalent geometry : bond 0.00408 (17114) covalent geometry : angle 0.67971 (24372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8258 (tp30) REVERT: B 63 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8201 (mt-10) REVERT: B 79 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8573 (mtpm) REVERT: D 90 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: G 73 ASN cc_start: 0.8669 (t0) cc_final: 0.8429 (t0) REVERT: H 48 ASP cc_start: 0.9057 (p0) cc_final: 0.8490 (p0) REVERT: K 91 LEU cc_start: 0.9132 (mp) cc_final: 0.8795 (pt) REVERT: K 219 LEU cc_start: 0.8897 (tt) cc_final: 0.8519 (tt) REVERT: K 605 ASP cc_start: 0.8971 (m-30) cc_final: 0.8728 (m-30) REVERT: K 647 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8286 (t70) REVERT: K 652 GLN cc_start: 0.8151 (mp10) cc_final: 0.7857 (mp10) outliers start: 20 outliers final: 9 residues processed: 205 average time/residue: 1.4807 time to fit residues: 330.7534 Evaluate side-chains 165 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 573 VAL Chi-restraints excluded: chain K residue 647 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 24 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 150 optimal weight: 0.0770 chunk 100 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN F 93 GLN ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS K 361 HIS K 471 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.094399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.067732 restraints weight = 42011.753| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.00 r_work: 0.3068 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17114 Z= 0.171 Angle : 0.637 9.039 24372 Z= 0.357 Chirality : 0.038 0.352 2769 Planarity : 0.005 0.072 2079 Dihedral : 30.066 176.441 4597 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 2.38 % Allowed : 17.78 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.41 (0.25), residues: 1253 helix: 1.62 (0.19), residues: 772 sheet: -2.04 (0.69), residues: 71 loop : -1.98 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 364 HIS 0.007 0.001 HIS K 402 PHE 0.035 0.002 PHE K 109 TYR 0.014 0.001 TYR K 320 ARG 0.016 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 925) hydrogen bonds : angle 3.28589 ( 2379) covalent geometry : bond 0.00384 (17114) covalent geometry : angle 0.63702 (24372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8025 (mp0) REVERT: B 63 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 77 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8410 (mptt) REVERT: C 90 ASP cc_start: 0.8469 (t0) cc_final: 0.8246 (t0) REVERT: E 73 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8520 (tm-30) REVERT: E 77 ASP cc_start: 0.8504 (m-30) cc_final: 0.8256 (m-30) REVERT: G 73 ASN cc_start: 0.8863 (t0) cc_final: 0.8509 (t160) REVERT: H 48 ASP cc_start: 0.9063 (p0) cc_final: 0.8553 (p0) REVERT: K 91 LEU cc_start: 0.9052 (mp) cc_final: 0.8727 (pt) REVERT: K 205 ASN cc_start: 0.8881 (m110) cc_final: 0.8457 (m110) REVERT: K 223 MET cc_start: 0.8482 (tmm) cc_final: 0.8121 (tmt) REVERT: K 433 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7561 (ttt) REVERT: K 647 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8504 (t70) REVERT: K 652 GLN cc_start: 0.8198 (mp10) cc_final: 0.7856 (mm110) outliers start: 26 outliers final: 9 residues processed: 197 average time/residue: 1.5297 time to fit residues: 329.1361 Evaluate side-chains 168 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 573 VAL Chi-restraints excluded: chain K residue 647 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 70 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 64 ASN C 84 GLN E 76 GLN ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063666 restraints weight = 42134.708| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.06 r_work: 0.2953 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17114 Z= 0.278 Angle : 0.694 8.773 24372 Z= 0.386 Chirality : 0.041 0.244 2769 Planarity : 0.006 0.144 2079 Dihedral : 30.289 177.071 4597 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 3.48 % Allowed : 18.79 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1253 helix: 1.46 (0.19), residues: 775 sheet: -2.09 (0.66), residues: 76 loop : -1.99 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 364 HIS 0.009 0.001 HIS K 402 PHE 0.026 0.002 PHE K 109 TYR 0.013 0.002 TYR K 320 ARG 0.025 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.05096 ( 925) hydrogen bonds : angle 3.50494 ( 2379) covalent geometry : bond 0.00639 (17114) covalent geometry : angle 0.69401 (24372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8381 (mt-10) REVERT: C 90 ASP cc_start: 0.8504 (t0) cc_final: 0.8259 (t0) REVERT: E 73 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8428 (tm-30) REVERT: E 122 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8467 (ptmm) REVERT: G 73 ASN cc_start: 0.9091 (t0) cc_final: 0.8652 (t0) REVERT: G 75 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8978 (mtpp) REVERT: G 104 GLN cc_start: 0.8598 (tp40) cc_final: 0.8364 (mm-40) REVERT: H 48 ASP cc_start: 0.9099 (p0) cc_final: 0.8655 (p0) REVERT: K 91 LEU cc_start: 0.9108 (mp) cc_final: 0.8774 (pt) REVERT: K 201 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7415 (mp) REVERT: K 205 ASN cc_start: 0.8868 (m110) cc_final: 0.8594 (m110) REVERT: K 412 ARG cc_start: 0.8180 (mmp80) cc_final: 0.7958 (mmm160) REVERT: K 605 ASP cc_start: 0.9220 (m-30) cc_final: 0.8828 (m-30) REVERT: K 647 ASP cc_start: 0.8990 (OUTLIER) cc_final: 0.8320 (t0) REVERT: K 652 GLN cc_start: 0.8347 (mp10) cc_final: 0.7959 (mp10) outliers start: 38 outliers final: 12 residues processed: 195 average time/residue: 1.5380 time to fit residues: 326.1025 Evaluate side-chains 168 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 573 VAL Chi-restraints excluded: chain K residue 647 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 59 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN B 93 GLN E 76 GLN ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.091776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.064477 restraints weight = 42652.110| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.06 r_work: 0.2973 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17114 Z= 0.229 Angle : 0.661 9.294 24372 Z= 0.369 Chirality : 0.039 0.183 2769 Planarity : 0.005 0.108 2079 Dihedral : 30.063 176.481 4597 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 3.21 % Allowed : 20.99 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1253 helix: 1.57 (0.19), residues: 773 sheet: -2.04 (0.66), residues: 76 loop : -1.94 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 267 HIS 0.008 0.001 HIS K 402 PHE 0.019 0.002 PHE K 109 TYR 0.013 0.002 TYR F 51 ARG 0.016 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 925) hydrogen bonds : angle 3.34524 ( 2379) covalent geometry : bond 0.00525 (17114) covalent geometry : angle 0.66071 (24372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8363 (mt-10) REVERT: C 90 ASP cc_start: 0.8455 (t0) cc_final: 0.8242 (t0) REVERT: D 30 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.4915 (tpm170) REVERT: E 73 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8430 (tm-30) REVERT: E 122 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8425 (ptmm) REVERT: G 73 ASN cc_start: 0.9043 (t0) cc_final: 0.8608 (t0) REVERT: G 75 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8940 (mtpp) REVERT: G 110 ASN cc_start: 0.9199 (t0) cc_final: 0.8999 (t0) REVERT: H 48 ASP cc_start: 0.9093 (p0) cc_final: 0.8633 (p0) REVERT: H 110 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8409 (tt0) REVERT: K 91 LEU cc_start: 0.9132 (mp) cc_final: 0.8807 (pt) REVERT: K 201 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7429 (mp) REVERT: K 205 ASN cc_start: 0.8903 (m110) cc_final: 0.8657 (m110) REVERT: K 229 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.8688 (tm) REVERT: K 493 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8122 (t) outliers start: 35 outliers final: 10 residues processed: 193 average time/residue: 1.5614 time to fit residues: 328.1470 Evaluate side-chains 174 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain K residue 229 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 150 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.094001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066504 restraints weight = 41765.837| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.13 r_work: 0.3003 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17114 Z= 0.152 Angle : 0.627 9.424 24372 Z= 0.352 Chirality : 0.037 0.164 2769 Planarity : 0.004 0.052 2079 Dihedral : 29.677 176.422 4597 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 1.28 % Allowed : 23.01 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.67 (0.25), residues: 1253 helix: 1.81 (0.19), residues: 771 sheet: -2.00 (0.71), residues: 64 loop : -1.85 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP K 267 HIS 0.009 0.001 HIS K 402 PHE 0.016 0.001 PHE K 109 TYR 0.010 0.001 TYR C 57 ARG 0.008 0.000 ARG K 262 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 925) hydrogen bonds : angle 3.12776 ( 2379) covalent geometry : bond 0.00339 (17114) covalent geometry : angle 0.62741 (24372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8429 (mt-10) REVERT: C 90 ASP cc_start: 0.8433 (t0) cc_final: 0.8122 (t0) REVERT: D 39 TYR cc_start: 0.8343 (t80) cc_final: 0.8105 (t80) REVERT: D 59 MET cc_start: 0.9116 (mmm) cc_final: 0.8781 (mmt) REVERT: E 73 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8516 (tm-30) REVERT: E 123 ASP cc_start: 0.8883 (m-30) cc_final: 0.8657 (m-30) REVERT: G 73 ASN cc_start: 0.9023 (t0) cc_final: 0.8492 (t0) REVERT: G 110 ASN cc_start: 0.9234 (t0) cc_final: 0.8992 (t0) REVERT: H 48 ASP cc_start: 0.9155 (p0) cc_final: 0.8724 (p0) REVERT: K 91 LEU cc_start: 0.9146 (mp) cc_final: 0.8800 (pt) REVERT: K 109 PHE cc_start: 0.8512 (m-10) cc_final: 0.7991 (m-80) REVERT: K 201 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7310 (mp) REVERT: K 205 ASN cc_start: 0.8895 (m110) cc_final: 0.8647 (m110) REVERT: K 400 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8450 (tm-30) REVERT: K 493 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8191 (t) outliers start: 14 outliers final: 4 residues processed: 193 average time/residue: 1.5422 time to fit residues: 323.8750 Evaluate side-chains 171 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 493 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 67 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 ASN K 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.093713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066265 restraints weight = 41785.470| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.13 r_work: 0.2994 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17114 Z= 0.163 Angle : 0.640 9.963 24372 Z= 0.356 Chirality : 0.037 0.294 2769 Planarity : 0.004 0.045 2079 Dihedral : 29.654 177.010 4597 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 1.65 % Allowed : 24.47 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.72 (0.25), residues: 1253 helix: 1.82 (0.19), residues: 777 sheet: -2.00 (0.71), residues: 64 loop : -1.81 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP K 267 HIS 0.011 0.001 HIS K 211 PHE 0.014 0.001 PHE K 109 TYR 0.016 0.001 TYR K 545 ARG 0.008 0.000 ARG K 529 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 925) hydrogen bonds : angle 3.13855 ( 2379) covalent geometry : bond 0.00367 (17114) covalent geometry : angle 0.63957 (24372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8445 (t0) cc_final: 0.8128 (t0) REVERT: D 39 TYR cc_start: 0.8402 (t80) cc_final: 0.8143 (t80) REVERT: E 73 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8497 (tm-30) REVERT: E 123 ASP cc_start: 0.8859 (m-30) cc_final: 0.8625 (m-30) REVERT: F 79 LYS cc_start: 0.9209 (ttmm) cc_final: 0.8880 (ttmm) REVERT: G 73 ASN cc_start: 0.9053 (t0) cc_final: 0.8518 (t0) REVERT: H 48 ASP cc_start: 0.9150 (p0) cc_final: 0.8729 (p0) REVERT: K 91 LEU cc_start: 0.9129 (mp) cc_final: 0.8783 (pt) REVERT: K 109 PHE cc_start: 0.8483 (m-10) cc_final: 0.7957 (m-80) REVERT: K 201 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7230 (mp) REVERT: K 205 ASN cc_start: 0.8942 (m-40) cc_final: 0.8685 (m110) REVERT: K 400 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: K 493 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8246 (t) outliers start: 18 outliers final: 10 residues processed: 186 average time/residue: 1.5095 time to fit residues: 306.2949 Evaluate side-chains 179 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.093018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065560 restraints weight = 42174.622| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.05 r_work: 0.2998 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17114 Z= 0.197 Angle : 0.668 10.735 24372 Z= 0.369 Chirality : 0.039 0.324 2769 Planarity : 0.004 0.052 2079 Dihedral : 29.719 177.000 4597 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 1.92 % Allowed : 24.66 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.67 (0.25), residues: 1253 helix: 1.78 (0.19), residues: 777 sheet: -1.93 (0.69), residues: 66 loop : -1.84 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP K 267 HIS 0.008 0.001 HIS K 402 PHE 0.015 0.001 PHE K 385 TYR 0.011 0.001 TYR F 51 ARG 0.010 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 925) hydrogen bonds : angle 3.25308 ( 2379) covalent geometry : bond 0.00452 (17114) covalent geometry : angle 0.66817 (24372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8395 (tt0) cc_final: 0.8065 (tp30) REVERT: C 90 ASP cc_start: 0.8455 (t0) cc_final: 0.8191 (t0) REVERT: D 39 TYR cc_start: 0.8408 (t80) cc_final: 0.8173 (t80) REVERT: E 73 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8532 (tm-30) REVERT: F 79 LYS cc_start: 0.9253 (ttmm) cc_final: 0.8951 (ttmm) REVERT: G 73 ASN cc_start: 0.9051 (t0) cc_final: 0.8597 (t0) REVERT: H 48 ASP cc_start: 0.9101 (p0) cc_final: 0.8670 (p0) REVERT: H 110 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: K 91 LEU cc_start: 0.9101 (mp) cc_final: 0.8779 (pt) REVERT: K 109 PHE cc_start: 0.8492 (m-10) cc_final: 0.7984 (m-80) REVERT: K 196 LEU cc_start: 0.8520 (tp) cc_final: 0.8223 (tp) REVERT: K 205 ASN cc_start: 0.8972 (m-40) cc_final: 0.8726 (m110) REVERT: K 385 PHE cc_start: 0.8053 (m-80) cc_final: 0.7462 (m-80) REVERT: K 400 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (tm-30) REVERT: K 493 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8251 (t) outliers start: 21 outliers final: 10 residues processed: 180 average time/residue: 1.5906 time to fit residues: 313.2795 Evaluate side-chains 177 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 94 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.093512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065933 restraints weight = 41712.453| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.12 r_work: 0.2984 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17114 Z= 0.176 Angle : 0.661 10.757 24372 Z= 0.365 Chirality : 0.038 0.286 2769 Planarity : 0.004 0.048 2079 Dihedral : 29.627 176.884 4597 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.70 % Favored : 93.22 % Rotamer: Outliers : 1.74 % Allowed : 24.93 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.69 (0.25), residues: 1253 helix: 1.81 (0.19), residues: 774 sheet: -1.99 (0.69), residues: 66 loop : -1.81 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP K 267 HIS 0.006 0.001 HIS K 211 PHE 0.017 0.001 PHE K 385 TYR 0.012 0.001 TYR K 199 ARG 0.010 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 925) hydrogen bonds : angle 3.20826 ( 2379) covalent geometry : bond 0.00401 (17114) covalent geometry : angle 0.66074 (24372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8529 (tt0) cc_final: 0.8322 (tp30) REVERT: C 90 ASP cc_start: 0.8474 (t0) cc_final: 0.8169 (t0) REVERT: D 39 TYR cc_start: 0.8349 (t80) cc_final: 0.8105 (t80) REVERT: D 59 MET cc_start: 0.9117 (mmm) cc_final: 0.8801 (mmt) REVERT: E 73 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8499 (tm-30) REVERT: F 79 LYS cc_start: 0.9289 (ttmm) cc_final: 0.8985 (ttmm) REVERT: G 73 ASN cc_start: 0.9081 (t0) cc_final: 0.8555 (t0) REVERT: H 48 ASP cc_start: 0.9170 (p0) cc_final: 0.8757 (p0) REVERT: H 110 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: K 91 LEU cc_start: 0.9116 (mp) cc_final: 0.8809 (pp) REVERT: K 109 PHE cc_start: 0.8490 (m-10) cc_final: 0.7971 (m-80) REVERT: K 196 LEU cc_start: 0.8579 (tp) cc_final: 0.8316 (tp) REVERT: K 385 PHE cc_start: 0.7946 (m-80) cc_final: 0.7396 (m-80) REVERT: K 400 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8442 (pp30) REVERT: K 433 MET cc_start: 0.8078 (ttt) cc_final: 0.7584 (tmm) REVERT: K 493 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8212 (t) outliers start: 19 outliers final: 10 residues processed: 184 average time/residue: 1.8518 time to fit residues: 373.4846 Evaluate side-chains 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 400 GLN Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 126 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 100 optimal weight: 0.0030 chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 141 optimal weight: 0.0070 chunk 55 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS ** K 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.095257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067939 restraints weight = 41955.353| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.16 r_work: 0.3030 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17114 Z= 0.151 Angle : 0.662 10.679 24372 Z= 0.363 Chirality : 0.037 0.274 2769 Planarity : 0.004 0.044 2079 Dihedral : 29.473 177.040 4597 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.70 % Favored : 93.22 % Rotamer: Outliers : 1.10 % Allowed : 25.39 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.78 (0.25), residues: 1253 helix: 1.86 (0.19), residues: 774 sheet: -1.96 (0.69), residues: 66 loop : -1.73 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP K 267 HIS 0.008 0.001 HIS K 111 PHE 0.025 0.001 PHE K 385 TYR 0.013 0.001 TYR K 545 ARG 0.010 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 925) hydrogen bonds : angle 3.17236 ( 2379) covalent geometry : bond 0.00338 (17114) covalent geometry : angle 0.66160 (24372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8040 (mp0) REVERT: C 90 ASP cc_start: 0.8418 (t0) cc_final: 0.8089 (t0) REVERT: D 39 TYR cc_start: 0.8306 (t80) cc_final: 0.8048 (t80) REVERT: D 59 MET cc_start: 0.9119 (mmm) cc_final: 0.8742 (mmt) REVERT: E 73 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8473 (tm-30) REVERT: F 79 LYS cc_start: 0.9245 (ttmm) cc_final: 0.9036 (ttmm) REVERT: G 73 ASN cc_start: 0.9021 (t0) cc_final: 0.8461 (t0) REVERT: H 48 ASP cc_start: 0.9178 (p0) cc_final: 0.8772 (p0) REVERT: K 91 LEU cc_start: 0.9104 (mp) cc_final: 0.8790 (pp) REVERT: K 109 PHE cc_start: 0.8557 (m-10) cc_final: 0.8057 (m-80) REVERT: K 196 LEU cc_start: 0.8555 (tp) cc_final: 0.8303 (tp) REVERT: K 211 HIS cc_start: 0.8958 (t-170) cc_final: 0.8613 (t70) REVERT: K 223 MET cc_start: 0.8598 (tmm) cc_final: 0.8390 (tmt) REVERT: K 320 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6814 (m-10) REVERT: K 493 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8176 (t) outliers start: 12 outliers final: 5 residues processed: 187 average time/residue: 1.6999 time to fit residues: 347.5626 Evaluate side-chains 173 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 129 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.095456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068147 restraints weight = 41791.723| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.16 r_work: 0.3037 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17114 Z= 0.153 Angle : 0.658 10.971 24372 Z= 0.363 Chirality : 0.037 0.262 2769 Planarity : 0.004 0.044 2079 Dihedral : 29.433 177.426 4597 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 0.82 % Allowed : 26.31 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.76 (0.25), residues: 1253 helix: 1.86 (0.19), residues: 772 sheet: -1.89 (0.69), residues: 66 loop : -1.76 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP K 267 HIS 0.005 0.001 HIS K 402 PHE 0.015 0.001 PHE K 385 TYR 0.010 0.001 TYR K 320 ARG 0.009 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 925) hydrogen bonds : angle 3.17187 ( 2379) covalent geometry : bond 0.00342 (17114) covalent geometry : angle 0.65801 (24372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11044.44 seconds wall clock time: 191 minutes 34.54 seconds (11494.54 seconds total)