Starting phenix.real_space_refine on Sat May 17 16:50:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo2_61641/05_2025/9jo2_61641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo2_61641/05_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_61641/05_2025/9jo2_61641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo2_61641/05_2025/9jo2_61641.map" model { file = "/net/cci-nas-00/data/ceres_data/9jo2_61641/05_2025/9jo2_61641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo2_61641/05_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-5687/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: 9.48, per 1000 atoms: 0.58 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: 4.17 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: 7.05 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: 8.57 Time building geometry restraints manager: 4.92 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 44.580 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.730 ------------------------------------------------------------------------------- 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 : 1.362 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: 1.5527 time to fit residues: 417.8828 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 : 1.272 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.094576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.067999 restraints weight = 42349.650| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.05 r_work: 0.3078 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 30.332 176.451 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 0.67972 (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 : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8261 (tp30) REVERT: B 63 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8199 (mt-10) REVERT: B 79 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8569 (mtpm) REVERT: D 90 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: G 73 ASN cc_start: 0.8666 (t0) cc_final: 0.8425 (t0) REVERT: H 48 ASP cc_start: 0.9057 (p0) cc_final: 0.8488 (p0) REVERT: K 91 LEU cc_start: 0.9136 (mp) cc_final: 0.8797 (pt) REVERT: K 219 LEU cc_start: 0.8897 (tt) cc_final: 0.8520 (tt) REVERT: K 380 ASP cc_start: 0.8857 (m-30) cc_final: 0.8653 (p0) REVERT: K 605 ASP cc_start: 0.8964 (m-30) cc_final: 0.8722 (m-30) REVERT: K 647 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8280 (t70) REVERT: K 652 GLN cc_start: 0.8146 (mp10) cc_final: 0.7852 (mp10) outliers start: 20 outliers final: 9 residues processed: 205 average time/residue: 1.4407 time to fit residues: 322.7055 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 : 1.367 ------------------------------------------------------------------------------- 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: 0.8980 chunk 143 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3772 r_free = 0.3772 target = 0.094634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068006 restraints weight = 42020.126| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.02 r_work: 0.3075 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3122 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= 0.166 Angle : 0.634 9.045 24372 Z= 0.356 Chirality : 0.038 0.343 2769 Planarity : 0.004 0.073 2079 Dihedral : 30.064 176.365 4597 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 2.47 % Allowed : 17.14 % Favored : 80.38 % 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: 0.42 (0.25), residues: 1253 helix: 1.63 (0.19), residues: 772 sheet: -2.03 (0.69), residues: 71 loop : -1.99 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 364 HIS 0.008 0.001 HIS K 402 PHE 0.034 0.001 PHE K 109 TYR 0.012 0.001 TYR K 320 ARG 0.011 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 925) hydrogen bonds : angle 3.28676 ( 2379) covalent geometry : bond 0.00374 (17114) covalent geometry : angle 0.63422 (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: 27 poor density : 184 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8008 (mp0) REVERT: A 94 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8272 (tp30) REVERT: B 63 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8249 (mt-10) REVERT: C 90 ASP cc_start: 0.8473 (t0) cc_final: 0.8237 (t0) REVERT: E 73 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8394 (tm-30) REVERT: E 77 ASP cc_start: 0.8454 (m-30) cc_final: 0.8217 (m-30) REVERT: G 73 ASN cc_start: 0.8794 (t0) cc_final: 0.8447 (t0) REVERT: H 48 ASP cc_start: 0.9059 (p0) cc_final: 0.8575 (p0) REVERT: K 91 LEU cc_start: 0.9051 (mp) cc_final: 0.8724 (pt) REVERT: K 205 ASN cc_start: 0.8887 (m110) cc_final: 0.8471 (m110) REVERT: K 223 MET cc_start: 0.8430 (tmm) cc_final: 0.8079 (tmt) REVERT: K 229 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.8857 (tm) REVERT: K 647 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8497 (t70) REVERT: K 652 GLN cc_start: 0.8172 (mp10) cc_final: 0.7839 (mm110) outliers start: 27 outliers final: 8 residues processed: 197 average time/residue: 1.4296 time to fit residues: 307.7046 Evaluate side-chains 163 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 58 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 K residue 229 LEU 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: 0.6980 chunk 66 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 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 = 0.3753 r_free = 0.3753 target = 0.093908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066860 restraints weight = 42337.522| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.08 r_work: 0.3029 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3677 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= 0.177 Angle : 0.628 8.876 24372 Z= 0.354 Chirality : 0.038 0.271 2769 Planarity : 0.005 0.094 2079 Dihedral : 29.905 176.467 4597 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 3.12 % Allowed : 19.16 % 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: 0.62 (0.25), residues: 1253 helix: 1.77 (0.19), residues: 768 sheet: -1.95 (0.69), residues: 71 loop : -1.83 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 267 HIS 0.009 0.001 HIS K 402 PHE 0.026 0.001 PHE K 109 TYR 0.011 0.001 TYR K 320 ARG 0.016 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 925) hydrogen bonds : angle 3.22684 ( 2379) covalent geometry : bond 0.00400 (17114) covalent geometry : angle 0.62816 (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: 34 poor density : 175 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8257 (tp30) REVERT: B 63 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 90 ASP cc_start: 0.8469 (t0) cc_final: 0.8244 (t0) REVERT: D 59 MET cc_start: 0.9082 (mmm) cc_final: 0.8635 (mmt) REVERT: E 73 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8424 (tm-30) REVERT: G 73 ASN cc_start: 0.8993 (t0) cc_final: 0.8535 (t0) REVERT: H 48 ASP cc_start: 0.9122 (p0) cc_final: 0.8670 (p0) REVERT: H 110 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: K 91 LEU cc_start: 0.9013 (mp) cc_final: 0.8675 (pt) REVERT: K 201 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7201 (mp) REVERT: K 205 ASN cc_start: 0.8813 (m110) cc_final: 0.8502 (m110) REVERT: K 229 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.8538 (tm) REVERT: K 266 ARG cc_start: 0.8941 (ptm-80) cc_final: 0.8561 (ptt90) REVERT: K 605 ASP cc_start: 0.9090 (m-30) cc_final: 0.8745 (m-30) REVERT: K 609 MET cc_start: 0.8915 (mpt) cc_final: 0.8703 (mpt) REVERT: K 647 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8272 (t0) REVERT: K 652 GLN cc_start: 0.8254 (mp10) cc_final: 0.7880 (mp10) outliers start: 34 outliers final: 11 residues processed: 196 average time/residue: 1.4720 time to fit residues: 314.5711 Evaluate side-chains 172 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 E residue 124 ILE Chi-restraints excluded: chain G residue 19 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 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 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: 1.9990 chunk 97 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.094820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067809 restraints weight = 42945.335| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.12 r_work: 0.3048 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3970 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= 0.158 Angle : 0.619 9.220 24372 Z= 0.348 Chirality : 0.037 0.185 2769 Planarity : 0.004 0.080 2079 Dihedral : 29.708 176.714 4597 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.30 % Rotamer: Outliers : 2.38 % Allowed : 21.17 % Favored : 76.44 % 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: 1.85 (0.19), residues: 772 sheet: -1.73 (0.73), residues: 66 loop : -1.87 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K 267 HIS 0.009 0.001 HIS K 402 PHE 0.020 0.001 PHE K 109 TYR 0.013 0.001 TYR D 37 ARG 0.013 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 925) hydrogen bonds : angle 3.09158 ( 2379) covalent geometry : bond 0.00353 (17114) covalent geometry : angle 0.61881 (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 203 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7958 (mp0) REVERT: A 94 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8177 (mt-10) REVERT: B 63 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8297 (mt-10) REVERT: C 90 ASP cc_start: 0.8413 (t0) cc_final: 0.8134 (t0) REVERT: C 95 LYS cc_start: 0.9103 (tppp) cc_final: 0.8850 (ttmm) REVERT: D 59 MET cc_start: 0.9114 (mmm) cc_final: 0.8651 (mmt) REVERT: E 73 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 76 GLN cc_start: 0.8627 (pt0) cc_final: 0.8380 (pp30) REVERT: E 123 ASP cc_start: 0.8853 (m-30) cc_final: 0.8587 (m-30) REVERT: F 80 THR cc_start: 0.9274 (m) cc_final: 0.9072 (p) REVERT: G 73 ASN cc_start: 0.8989 (t0) cc_final: 0.8476 (t0) REVERT: G 104 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8346 (mm110) REVERT: H 48 ASP cc_start: 0.9125 (p0) cc_final: 0.8677 (p0) REVERT: K 91 LEU cc_start: 0.8886 (mp) cc_final: 0.8515 (pp) REVERT: K 221 ASP cc_start: 0.8880 (m-30) cc_final: 0.8677 (m-30) REVERT: K 493 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8134 (t) REVERT: K 605 ASP cc_start: 0.9115 (m-30) cc_final: 0.8723 (m-30) REVERT: K 609 MET cc_start: 0.8868 (mpt) cc_final: 0.8607 (mpp) outliers start: 26 outliers final: 13 residues processed: 192 average time/residue: 1.4462 time to fit residues: 304.5159 Evaluate side-chains 176 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 610 ASP 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: 7.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN B 75 HIS ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 ASN K 327 HIS ** K 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.091232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.063569 restraints weight = 42407.261| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.09 r_work: 0.2949 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 17114 Z= 0.285 Angle : 0.697 9.674 24372 Z= 0.388 Chirality : 0.041 0.262 2769 Planarity : 0.005 0.124 2079 Dihedral : 30.068 177.434 4597 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 2.66 % Allowed : 22.73 % Favored : 74.61 % 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: 0.47 (0.25), residues: 1253 helix: 1.61 (0.19), residues: 771 sheet: -1.97 (0.66), residues: 76 loop : -1.84 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP K 267 HIS 0.009 0.001 HIS K 402 PHE 0.019 0.002 PHE K 109 TYR 0.013 0.002 TYR F 51 ARG 0.022 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.05037 ( 925) hydrogen bonds : angle 3.43800 ( 2379) covalent geometry : bond 0.00661 (17114) covalent geometry : angle 0.69743 (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 194 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8372 (tp30) REVERT: B 63 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8388 (mt-10) REVERT: B 77 LYS cc_start: 0.8520 (mptt) cc_final: 0.8296 (mptt) REVERT: C 90 ASP cc_start: 0.8537 (t0) cc_final: 0.8316 (t0) REVERT: C 95 LYS cc_start: 0.9132 (tppp) cc_final: 0.8841 (tppp) REVERT: D 30 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.4759 (tpm170) REVERT: E 73 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8516 (tm-30) REVERT: G 73 ASN cc_start: 0.9082 (t0) cc_final: 0.8599 (t0) REVERT: H 48 ASP cc_start: 0.9104 (p0) cc_final: 0.8654 (p0) REVERT: H 110 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: K 91 LEU cc_start: 0.9012 (mp) cc_final: 0.8642 (pt) REVERT: K 266 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8477 (ptm-80) REVERT: K 493 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8090 (t) REVERT: K 605 ASP cc_start: 0.9160 (m-30) cc_final: 0.8765 (m-30) REVERT: K 609 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8549 (mpp) outliers start: 29 outliers final: 13 residues processed: 185 average time/residue: 1.5286 time to fit residues: 307.8231 Evaluate side-chains 164 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 101 THR Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 266 ARG Chi-restraints excluded: chain K residue 350 LEU Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.094809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067408 restraints weight = 42014.736| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.16 r_work: 0.3020 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17114 Z= 0.148 Angle : 0.627 9.717 24372 Z= 0.353 Chirality : 0.037 0.267 2769 Planarity : 0.004 0.045 2079 Dihedral : 29.561 176.154 4597 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.14 % Rotamer: Outliers : 1.65 % Allowed : 23.83 % Favored : 74.52 % 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: 0.73 (0.25), residues: 1253 helix: 1.84 (0.19), residues: 771 sheet: -2.05 (0.70), residues: 64 loop : -1.75 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 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 0.007 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 925) hydrogen bonds : angle 3.12608 ( 2379) covalent geometry : bond 0.00329 (17114) covalent geometry : angle 0.62726 (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 200 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.420 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: A 50 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8001 (mp0) REVERT: A 94 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8195 (mt-10) REVERT: A 105 GLU cc_start: 0.8472 (tt0) cc_final: 0.8218 (tp30) REVERT: B 27 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: B 63 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8430 (mt-10) REVERT: C 90 ASP cc_start: 0.8445 (t0) cc_final: 0.8126 (t0) REVERT: C 95 LYS cc_start: 0.9185 (tppp) cc_final: 0.8883 (tppp) REVERT: D 59 MET cc_start: 0.9148 (mmm) cc_final: 0.8801 (mmt) REVERT: D 65 ASP cc_start: 0.8992 (t0) cc_final: 0.8791 (t0) REVERT: E 73 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8384 (tm-30) REVERT: E 123 ASP cc_start: 0.8872 (m-30) cc_final: 0.8589 (m-30) REVERT: G 73 ASN cc_start: 0.9038 (t0) cc_final: 0.8478 (t0) REVERT: H 48 ASP cc_start: 0.9168 (p0) cc_final: 0.8742 (p0) REVERT: K 91 LEU cc_start: 0.8962 (mp) cc_final: 0.8548 (pp) REVERT: K 109 PHE cc_start: 0.8539 (m-10) cc_final: 0.7993 (m-80) REVERT: K 266 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8606 (ptm-80) REVERT: K 493 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8023 (t) REVERT: K 605 ASP cc_start: 0.9209 (m-30) cc_final: 0.8761 (m-30) REVERT: K 609 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8513 (mpp) outliers start: 18 outliers final: 8 residues processed: 191 average time/residue: 1.4698 time to fit residues: 306.7631 Evaluate side-chains 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 266 ARG Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 610 ASP 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: 0.9990 chunk 38 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** K 111 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 = 0.3706 r_free = 0.3706 target = 0.091321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064001 restraints weight = 42123.356| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.04 r_work: 0.2961 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17114 Z= 0.261 Angle : 0.688 10.253 24372 Z= 0.383 Chirality : 0.040 0.267 2769 Planarity : 0.005 0.045 2079 Dihedral : 29.935 177.571 4597 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.02 % Favored : 92.90 % Rotamer: Outliers : 2.20 % Allowed : 24.38 % 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: 0.47 (0.25), residues: 1253 helix: 1.59 (0.19), residues: 779 sheet: -1.79 (0.66), residues: 73 loop : -1.89 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP K 267 HIS 0.008 0.001 HIS K 402 PHE 0.016 0.002 PHE K 385 TYR 0.023 0.002 TYR K 199 ARG 0.007 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 925) hydrogen bonds : angle 3.38435 ( 2379) covalent geometry : bond 0.00603 (17114) covalent geometry : angle 0.68827 (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 191 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8370 (tp30) REVERT: B 63 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8405 (mt-10) REVERT: B 77 LYS cc_start: 0.8544 (mptt) cc_final: 0.8339 (mptt) REVERT: C 90 ASP cc_start: 0.8507 (t0) cc_final: 0.8285 (t0) REVERT: C 95 LYS cc_start: 0.9163 (tppp) cc_final: 0.8920 (tppp) REVERT: E 73 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8557 (tm-30) REVERT: F 79 LYS cc_start: 0.9266 (ttmm) cc_final: 0.8937 (ttmm) REVERT: G 73 ASN cc_start: 0.9090 (t0) cc_final: 0.8622 (t0) REVERT: H 48 ASP cc_start: 0.9094 (p0) cc_final: 0.8661 (p0) REVERT: K 91 LEU cc_start: 0.8932 (mp) cc_final: 0.8536 (pp) REVERT: K 109 PHE cc_start: 0.8543 (m-10) cc_final: 0.8028 (m-80) REVERT: K 223 MET cc_start: 0.8530 (tmt) cc_final: 0.8263 (tmm) REVERT: K 266 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8717 (ptm-80) REVERT: K 493 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8304 (t) REVERT: K 605 ASP cc_start: 0.9123 (m-30) cc_final: 0.8760 (m-30) REVERT: K 609 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8503 (mpp) REVERT: K 610 ASP cc_start: 0.9111 (t0) cc_final: 0.8908 (t0) outliers start: 24 outliers final: 10 residues processed: 184 average time/residue: 1.4945 time to fit residues: 299.8984 Evaluate side-chains 170 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR 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 G residue 101 THR Chi-restraints excluded: chain K residue 266 ARG Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 350 LEU Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 609 MET 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: 20.0000 chunk 107 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.092436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064621 restraints weight = 41796.603| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.13 r_work: 0.2953 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17114 Z= 0.201 Angle : 0.665 9.789 24372 Z= 0.371 Chirality : 0.039 0.287 2769 Planarity : 0.004 0.053 2079 Dihedral : 29.770 176.593 4597 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 1.83 % Allowed : 25.66 % Favored : 72.50 % 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: 0.52 (0.25), residues: 1253 helix: 1.65 (0.19), residues: 778 sheet: -1.82 (0.70), residues: 66 loop : -1.89 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP K 267 HIS 0.008 0.001 HIS K 402 PHE 0.015 0.001 PHE K 385 TYR 0.021 0.001 TYR K 199 ARG 0.011 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 925) hydrogen bonds : angle 3.26457 ( 2379) covalent geometry : bond 0.00461 (17114) covalent geometry : angle 0.66477 (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 191 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8383 (tp30) REVERT: B 63 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 77 LYS cc_start: 0.8494 (mptt) cc_final: 0.8287 (mptt) REVERT: C 90 ASP cc_start: 0.8447 (t0) cc_final: 0.8164 (t0) REVERT: C 95 LYS cc_start: 0.9142 (tppp) cc_final: 0.8926 (tppp) REVERT: E 73 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8551 (tm-30) REVERT: F 79 LYS cc_start: 0.9306 (ttmm) cc_final: 0.8968 (ttmm) REVERT: G 73 ASN cc_start: 0.9083 (t0) cc_final: 0.8584 (t0) REVERT: G 110 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8976 (t0) REVERT: H 48 ASP cc_start: 0.9159 (p0) cc_final: 0.8724 (p0) REVERT: H 110 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8446 (tt0) REVERT: K 91 LEU cc_start: 0.8975 (mp) cc_final: 0.8551 (pp) REVERT: K 109 PHE cc_start: 0.8574 (m-10) cc_final: 0.8058 (m-80) REVERT: K 223 MET cc_start: 0.8405 (tmt) cc_final: 0.8085 (tmm) REVERT: K 266 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8760 (ptm-80) REVERT: K 385 PHE cc_start: 0.8271 (m-80) cc_final: 0.7384 (m-80) REVERT: K 493 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8263 (t) REVERT: K 605 ASP cc_start: 0.9176 (m-30) cc_final: 0.8761 (m-30) REVERT: K 609 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8556 (mpp) REVERT: K 610 ASP cc_start: 0.9062 (t0) cc_final: 0.8859 (t0) outliers start: 20 outliers final: 10 residues processed: 181 average time/residue: 1.4371 time to fit residues: 285.2938 Evaluate side-chains 180 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 73 THR 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 G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain K residue 266 ARG Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 350 LEU Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 609 MET 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: 0.7980 chunk 112 optimal weight: 0.3980 chunk 150 optimal weight: 0.6980 chunk 100 optimal weight: 0.0370 chunk 125 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 141 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 overall best weight: 0.2976 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.096454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.069386 restraints weight = 42141.239| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.17 r_work: 0.3070 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17114 Z= 0.147 Angle : 0.649 10.764 24372 Z= 0.362 Chirality : 0.037 0.274 2769 Planarity : 0.004 0.055 2079 Dihedral : 29.371 176.807 4597 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.37 % Allowed : 26.03 % Favored : 72.59 % 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: 0.80 (0.25), residues: 1253 helix: 1.88 (0.19), residues: 775 sheet: -1.76 (0.71), residues: 66 loop : -1.80 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.006 TRP K 384 HIS 0.007 0.001 HIS K 402 PHE 0.014 0.001 PHE K 385 TYR 0.020 0.001 TYR K 199 ARG 0.017 0.001 ARG K 655 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 925) hydrogen bonds : angle 3.06126 ( 2379) covalent geometry : bond 0.00324 (17114) covalent geometry : angle 0.64912 (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 209 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 1.292 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: 0.8405 (mt-10) cc_final: 0.8039 (mp0) REVERT: A 94 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8221 (mt-10) REVERT: A 105 GLU cc_start: 0.8442 (tt0) cc_final: 0.8170 (tp30) REVERT: B 27 GLN cc_start: 0.8791 (mp10) cc_final: 0.8201 (mp10) REVERT: C 90 ASP cc_start: 0.8385 (t0) cc_final: 0.8031 (t0) REVERT: C 95 LYS cc_start: 0.9141 (tppp) cc_final: 0.8937 (tppp) REVERT: D 59 MET cc_start: 0.9155 (mmm) cc_final: 0.8782 (mmt) REVERT: E 73 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8423 (tm-30) REVERT: G 73 ASN cc_start: 0.8921 (t0) cc_final: 0.8361 (t0) REVERT: H 48 ASP cc_start: 0.9184 (p0) cc_final: 0.8797 (p0) REVERT: K 91 LEU cc_start: 0.8898 (mp) cc_final: 0.8468 (pp) REVERT: K 109 PHE cc_start: 0.8439 (m-10) cc_final: 0.7918 (m-80) REVERT: K 223 MET cc_start: 0.8215 (tmt) cc_final: 0.7840 (tmm) REVERT: K 266 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8697 (ttp80) REVERT: K 385 PHE cc_start: 0.7956 (m-80) cc_final: 0.7525 (m-80) REVERT: K 493 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8090 (t) REVERT: K 605 ASP cc_start: 0.9147 (m-30) cc_final: 0.8709 (m-30) REVERT: K 609 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8591 (mpp) outliers start: 15 outliers final: 6 residues processed: 202 average time/residue: 1.4216 time to fit residues: 313.9601 Evaluate side-chains 181 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 87 SER Chi-restraints excluded: chain K residue 266 ARG Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 493 THR Chi-restraints excluded: chain K residue 609 MET 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: 0.9980 chunk 49 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.095562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068419 restraints weight = 41913.702| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.14 r_work: 0.3045 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17114 Z= 0.154 Angle : 0.657 10.439 24372 Z= 0.363 Chirality : 0.037 0.272 2769 Planarity : 0.004 0.053 2079 Dihedral : 29.442 177.532 4597 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 1.10 % Allowed : 27.22 % Favored : 71.68 % 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: 0.83 (0.25), residues: 1253 helix: 1.87 (0.19), residues: 779 sheet: -1.66 (0.72), residues: 66 loop : -1.75 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP K 267 HIS 0.009 0.001 HIS K 402 PHE 0.022 0.001 PHE K 119 TYR 0.020 0.001 TYR K 199 ARG 0.012 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 925) hydrogen bonds : angle 3.10700 ( 2379) covalent geometry : bond 0.00347 (17114) covalent geometry : angle 0.65719 (24372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9743.77 seconds wall clock time: 168 minutes 15.67 seconds (10095.67 seconds total)