Starting phenix.real_space_refine on Thu Sep 18 10:04:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jo2_61641/09_2025/9jo2_61641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jo2_61641/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jo2_61641/09_2025/9jo2_61641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jo2_61641/09_2025/9jo2_61641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jo2_61641/09_2025/9jo2_61641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jo2_61641/09_2025/9jo2_61641.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.42, per 1000 atoms: 0.21 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: 1.11 Conformation dependent library (CDL) restraints added in 393.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.31 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: 3.62 Time building geometry restraints manager: 1.51 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.600 ------------------------------------------------------------------------------- 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 : 15.83 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.019 0.001 ARG G 77 TYR 0.025 0.002 TYR K 320 PHE 0.024 0.002 PHE K 574 TRP 0.031 0.003 TRP K 267 HIS 0.008 0.002 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00952 (17114) covalent geometry : angle 0.84192 (24372) hydrogen bonds : bond 0.09812 ( 925) hydrogen bonds : angle 4.68746 ( 2379) *********************** 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 : 0.485 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: 0.7664 time to fit residues: 205.1049 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 : 0.465 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.094144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067581 restraints weight = 42478.108| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.04 r_work: 0.3067 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17114 Z= 0.195 Angle : 0.688 9.508 24372 Z= 0.384 Chirality : 0.040 0.203 2769 Planarity : 0.005 0.086 2079 Dihedral : 30.350 176.443 4599 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 2.29 % Allowed : 14.12 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.25), residues: 1253 helix: 1.35 (0.19), residues: 770 sheet: -2.06 (0.70), residues: 71 loop : -2.10 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 30 TYR 0.017 0.001 TYR K 320 PHE 0.045 0.002 PHE K 109 TRP 0.014 0.002 TRP K 364 HIS 0.007 0.001 HIS K 111 Details of bonding type rmsd covalent geometry : bond 0.00439 (17114) covalent geometry : angle 0.68811 (24372) hydrogen bonds : bond 0.04498 ( 925) hydrogen bonds : angle 3.60058 ( 2379) *********************** 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 220 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8217 (tp30) REVERT: B 63 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8292 (mt-10) REVERT: B 79 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8583 (mtpm) REVERT: D 90 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: G 73 ASN cc_start: 0.8690 (t0) cc_final: 0.8420 (t0) REVERT: H 48 ASP cc_start: 0.9075 (p0) cc_final: 0.8532 (p0) REVERT: H 110 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: K 91 LEU cc_start: 0.9147 (mp) cc_final: 0.8804 (pt) REVERT: K 380 ASP cc_start: 0.8847 (m-30) cc_final: 0.8641 (p0) outliers start: 25 outliers final: 11 residues processed: 208 average time/residue: 0.7486 time to fit residues: 168.7533 Evaluate side-chains 167 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 90 GLU Chi-restraints excluded: chain E residue 87 SER 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 421 LEU Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 573 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 21 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.094655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.067970 restraints weight = 42361.999| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.04 r_work: 0.3077 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3275 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= 0.165 Angle : 0.632 8.988 24372 Z= 0.354 Chirality : 0.038 0.164 2769 Planarity : 0.005 0.069 2079 Dihedral : 30.024 176.282 4599 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 2.75 % Allowed : 17.32 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1253 helix: 1.67 (0.19), residues: 772 sheet: -2.07 (0.68), residues: 71 loop : -1.96 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 30 TYR 0.012 0.001 TYR K 320 PHE 0.035 0.002 PHE K 109 TRP 0.010 0.001 TRP K 364 HIS 0.008 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00369 (17114) covalent geometry : angle 0.63166 (24372) hydrogen bonds : bond 0.03982 ( 925) hydrogen bonds : angle 3.25424 ( 2379) *********************** 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 218 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.9229 (tptt) cc_final: 0.9004 (tmtm) REVERT: B 63 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 77 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8366 (mptt) REVERT: C 90 ASP cc_start: 0.8445 (t0) cc_final: 0.8227 (t0) REVERT: E 73 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8466 (tm-30) REVERT: G 73 ASN cc_start: 0.8842 (t0) cc_final: 0.8493 (t160) REVERT: H 48 ASP cc_start: 0.9066 (p0) cc_final: 0.8583 (p0) REVERT: K 91 LEU cc_start: 0.9061 (mp) cc_final: 0.8731 (pt) REVERT: K 205 ASN cc_start: 0.8873 (m110) cc_final: 0.8452 (m110) REVERT: K 229 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.8790 (tm) REVERT: K 433 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7483 (ttt) REVERT: K 605 ASP cc_start: 0.9056 (m-30) cc_final: 0.8753 (m-30) outliers start: 30 outliers final: 9 residues processed: 201 average time/residue: 0.7332 time to fit residues: 160.0021 Evaluate side-chains 169 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 229 LEU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 573 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN E 76 GLN K 111 HIS ** 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 = 0.3759 r_free = 0.3759 target = 0.094244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.067246 restraints weight = 42497.676| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.09 r_work: 0.3035 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3646 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= 0.170 Angle : 0.627 8.936 24372 Z= 0.352 Chirality : 0.038 0.191 2769 Planarity : 0.005 0.090 2079 Dihedral : 29.896 176.429 4599 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.86 % Favored : 93.06 % Rotamer: Outliers : 2.38 % Allowed : 19.98 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1253 helix: 1.77 (0.19), residues: 769 sheet: -1.91 (0.69), residues: 71 loop : -1.86 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 30 TYR 0.017 0.001 TYR K 199 PHE 0.025 0.001 PHE K 109 TRP 0.028 0.002 TRP K 267 HIS 0.008 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00382 (17114) covalent geometry : angle 0.62704 (24372) hydrogen bonds : bond 0.03995 ( 925) hydrogen bonds : angle 3.22018 ( 2379) *********************** 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 205 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8341 (mt-10) REVERT: C 90 ASP cc_start: 0.8447 (t0) cc_final: 0.8210 (t0) REVERT: C 95 LYS cc_start: 0.9087 (tppp) cc_final: 0.8843 (ttmm) REVERT: D 56 MET cc_start: 0.8710 (tpp) cc_final: 0.7957 (tpt) REVERT: E 73 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8500 (tm-30) REVERT: E 122 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8442 (ptmm) REVERT: E 123 ASP cc_start: 0.8848 (m-30) cc_final: 0.8589 (m-30) REVERT: F 80 THR cc_start: 0.9281 (m) cc_final: 0.9022 (p) REVERT: G 73 ASN cc_start: 0.8952 (t0) cc_final: 0.8423 (t0) REVERT: G 104 GLN cc_start: 0.8437 (tp40) cc_final: 0.8230 (mm-40) REVERT: H 48 ASP cc_start: 0.9127 (p0) cc_final: 0.8664 (p0) REVERT: K 91 LEU cc_start: 0.9063 (mp) cc_final: 0.8724 (pt) REVERT: K 201 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7169 (mp) REVERT: K 205 ASN cc_start: 0.8832 (m110) cc_final: 0.8505 (m110) outliers start: 26 outliers final: 11 residues processed: 192 average time/residue: 0.7234 time to fit residues: 150.5914 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 : 0.414 ------------------------------------------------------------------------------- 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 122 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 644 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 133 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 127 optimal weight: 0.0770 chunk 45 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 K 205 ASN K 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.096277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068900 restraints weight = 42201.743| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.19 r_work: 0.3057 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4013 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= 0.145 Angle : 0.615 9.042 24372 Z= 0.346 Chirality : 0.037 0.163 2769 Planarity : 0.004 0.064 2079 Dihedral : 29.581 176.610 4599 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.93 % Allowed : 21.45 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.25), residues: 1253 helix: 1.91 (0.19), residues: 768 sheet: -1.03 (0.80), residues: 57 loop : -1.88 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.012 0.001 TYR K 199 PHE 0.020 0.001 PHE K 109 TRP 0.037 0.002 TRP K 267 HIS 0.006 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00317 (17114) covalent geometry : angle 0.61516 (24372) hydrogen bonds : bond 0.03608 ( 925) hydrogen bonds : angle 3.07599 ( 2379) *********************** 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 219 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: B 63 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 90 ASP cc_start: 0.8393 (t0) cc_final: 0.8093 (t0) REVERT: C 95 LYS cc_start: 0.9167 (tppp) cc_final: 0.8847 (ttmm) REVERT: C 99 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8231 (mmm160) REVERT: D 59 MET cc_start: 0.9075 (mmm) cc_final: 0.8638 (mmt) REVERT: E 73 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8416 (tm-30) REVERT: G 73 ASN cc_start: 0.8944 (t0) cc_final: 0.8432 (t0) REVERT: H 48 ASP cc_start: 0.9180 (p0) cc_final: 0.8753 (p0) REVERT: K 91 LEU cc_start: 0.8840 (mp) cc_final: 0.8429 (pp) REVERT: K 109 PHE cc_start: 0.8531 (m-10) cc_final: 0.8053 (m-80) REVERT: K 221 ASP cc_start: 0.8842 (m-30) cc_final: 0.8561 (m-30) REVERT: K 493 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8060 (t) outliers start: 32 outliers final: 12 residues processed: 207 average time/residue: 0.6693 time to fit residues: 151.0572 Evaluate side-chains 181 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 43 VAL 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 15 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 421 LEU 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 120 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN K 205 ASN K 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.095926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068463 restraints weight = 42201.251| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.18 r_work: 0.3044 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17114 Z= 0.153 Angle : 0.627 9.076 24372 Z= 0.348 Chirality : 0.037 0.281 2769 Planarity : 0.004 0.068 2079 Dihedral : 29.559 177.115 4599 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 2.02 % Allowed : 23.01 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.25), residues: 1253 helix: 1.94 (0.19), residues: 769 sheet: -1.04 (0.79), residues: 57 loop : -1.84 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.009 0.001 TYR K 199 PHE 0.016 0.001 PHE K 109 TRP 0.022 0.002 TRP K 267 HIS 0.008 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00343 (17114) covalent geometry : angle 0.62726 (24372) hydrogen bonds : bond 0.03677 ( 925) hydrogen bonds : angle 3.10506 ( 2379) *********************** 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 199 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.9035 (t0) cc_final: 0.8771 (t0) REVERT: B 27 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: C 90 ASP cc_start: 0.8367 (t0) cc_final: 0.8036 (t0) REVERT: C 95 LYS cc_start: 0.9171 (tppp) cc_final: 0.8951 (tppp) REVERT: E 73 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8376 (tm-30) REVERT: E 123 ASP cc_start: 0.8840 (m-30) cc_final: 0.8603 (m-30) REVERT: G 73 ASN cc_start: 0.9010 (t0) cc_final: 0.8483 (t0) REVERT: H 48 ASP cc_start: 0.9194 (p0) cc_final: 0.8784 (p0) REVERT: K 91 LEU cc_start: 0.8837 (mp) cc_final: 0.8416 (pp) REVERT: K 266 ARG cc_start: 0.9112 (ttt90) cc_final: 0.8789 (tpt90) REVERT: K 493 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.7994 (t) outliers start: 22 outliers final: 7 residues processed: 191 average time/residue: 0.6893 time to fit residues: 143.6734 Evaluate side-chains 175 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 27 GLN 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 64 GLU Chi-restraints excluded: chain K residue 421 LEU Chi-restraints excluded: chain K residue 493 THR 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 74 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS K 211 HIS K 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.093233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066030 restraints weight = 42111.121| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.07 r_work: 0.3009 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17114 Z= 0.200 Angle : 0.658 10.007 24372 Z= 0.364 Chirality : 0.039 0.239 2769 Planarity : 0.005 0.093 2079 Dihedral : 29.719 177.436 4599 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.18 % Favored : 92.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.25), residues: 1253 helix: 1.77 (0.19), residues: 778 sheet: -1.63 (0.69), residues: 71 loop : -1.67 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 30 TYR 0.011 0.001 TYR K 199 PHE 0.016 0.001 PHE K 109 TRP 0.038 0.003 TRP K 267 HIS 0.008 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00458 (17114) covalent geometry : angle 0.65841 (24372) hydrogen bonds : bond 0.04276 ( 925) hydrogen bonds : angle 3.25010 ( 2379) *********************** 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 194 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8486 (tt0) cc_final: 0.8188 (tt0) REVERT: A 94 GLU cc_start: 0.8375 (tt0) cc_final: 0.7859 (tp30) REVERT: B 77 LYS cc_start: 0.8457 (mptt) cc_final: 0.8240 (mptt) REVERT: C 90 ASP cc_start: 0.8512 (t0) cc_final: 0.8210 (t0) REVERT: C 95 LYS cc_start: 0.9148 (tppp) cc_final: 0.8886 (tppp) REVERT: D 30 ARG cc_start: 0.5518 (OUTLIER) cc_final: 0.4569 (tpm170) REVERT: D 59 MET cc_start: 0.9088 (mmm) cc_final: 0.8656 (mmt) REVERT: E 73 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8541 (tm-30) REVERT: F 79 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8945 (ttmm) REVERT: G 73 ASN cc_start: 0.9083 (t0) cc_final: 0.8579 (t0) REVERT: H 48 ASP cc_start: 0.9129 (p0) cc_final: 0.8713 (p0) REVERT: H 110 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: K 91 LEU cc_start: 0.8828 (mp) cc_final: 0.8421 (pp) REVERT: K 109 PHE cc_start: 0.8449 (m-10) cc_final: 0.7924 (m-80) REVERT: K 493 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8055 (t) REVERT: K 605 ASP cc_start: 0.9083 (m-30) cc_final: 0.8798 (m-30) outliers start: 24 outliers final: 10 residues processed: 186 average time/residue: 0.7243 time to fit residues: 146.1259 Evaluate side-chains 173 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 19 SER 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 316 ILE Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 421 LEU 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 38 optimal weight: 0.3980 chunk 123 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 54 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 K 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.094698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067354 restraints weight = 41972.562| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.12 r_work: 0.3017 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4462 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= 0.154 Angle : 0.646 12.440 24372 Z= 0.356 Chirality : 0.037 0.241 2769 Planarity : 0.004 0.067 2079 Dihedral : 29.548 177.409 4599 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.70 % Favored : 93.22 % Rotamer: Outliers : 1.65 % Allowed : 25.21 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.25), residues: 1253 helix: 1.84 (0.19), residues: 774 sheet: -1.57 (0.72), residues: 66 loop : -1.62 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 30 TYR 0.010 0.001 TYR C 57 PHE 0.013 0.001 PHE K 109 TRP 0.059 0.003 TRP K 267 HIS 0.008 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00343 (17114) covalent geometry : angle 0.64558 (24372) hydrogen bonds : bond 0.03751 ( 925) hydrogen bonds : angle 3.16078 ( 2379) *********************** 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: 18 poor density : 173 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8382 (tt0) cc_final: 0.7737 (tp30) REVERT: C 90 ASP cc_start: 0.8422 (t0) cc_final: 0.8069 (t0) REVERT: C 95 LYS cc_start: 0.9180 (tppp) cc_final: 0.8916 (tppp) REVERT: D 59 MET cc_start: 0.9102 (mmm) cc_final: 0.8755 (mmt) REVERT: E 73 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8505 (tm-30) REVERT: F 79 LYS cc_start: 0.9275 (ttmm) cc_final: 0.9038 (ttmm) REVERT: G 73 ASN cc_start: 0.9054 (t0) cc_final: 0.8542 (t0) REVERT: H 48 ASP cc_start: 0.9174 (p0) cc_final: 0.8762 (p0) REVERT: K 91 LEU cc_start: 0.8794 (mp) cc_final: 0.8391 (pp) REVERT: K 385 PHE cc_start: 0.8127 (m-80) cc_final: 0.7040 (m-80) REVERT: K 493 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8222 (t) outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 0.6497 time to fit residues: 128.3461 Evaluate side-chains 178 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 MET 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 64 GLU Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 421 LEU 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 145 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 100 optimal weight: 0.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.093599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065981 restraints weight = 41912.159| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.12 r_work: 0.2988 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4481 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= 0.186 Angle : 0.664 11.729 24372 Z= 0.366 Chirality : 0.038 0.230 2769 Planarity : 0.004 0.048 2079 Dihedral : 29.606 177.347 4599 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.02 % Favored : 92.90 % Rotamer: Outliers : 1.65 % Allowed : 25.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1253 helix: 1.81 (0.19), residues: 773 sheet: -1.53 (0.70), residues: 71 loop : -1.71 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.013 0.001 TYR K 545 PHE 0.015 0.001 PHE K 119 TRP 0.057 0.004 TRP K 267 HIS 0.007 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00423 (17114) covalent geometry : angle 0.66433 (24372) hydrogen bonds : bond 0.04047 ( 925) hydrogen bonds : angle 3.21437 ( 2379) *********************** 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 185 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8403 (tt0) cc_final: 0.7849 (tp30) REVERT: C 90 ASP cc_start: 0.8473 (t0) cc_final: 0.8164 (t0) REVERT: C 95 LYS cc_start: 0.9170 (tppp) cc_final: 0.8919 (tppp) REVERT: D 59 MET cc_start: 0.9102 (mmm) cc_final: 0.8768 (mmt) REVERT: E 73 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8552 (tm-30) REVERT: F 79 LYS cc_start: 0.9293 (ttmm) cc_final: 0.9052 (ttmm) REVERT: G 73 ASN cc_start: 0.9096 (t0) cc_final: 0.8583 (t0) REVERT: H 48 ASP cc_start: 0.9167 (p0) cc_final: 0.8763 (p0) REVERT: K 91 LEU cc_start: 0.8818 (mp) cc_final: 0.8425 (pp) REVERT: K 109 PHE cc_start: 0.8433 (m-10) cc_final: 0.7865 (m-80) REVERT: K 223 MET cc_start: 0.8677 (tmm) cc_final: 0.8393 (tmm) REVERT: K 493 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8174 (t) REVERT: K 647 ASP cc_start: 0.9232 (p0) cc_final: 0.9030 (p0) outliers start: 18 outliers final: 11 residues processed: 176 average time/residue: 0.6696 time to fit residues: 128.1113 Evaluate side-chains 174 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL 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 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 K residue 316 ILE Chi-restraints excluded: chain K residue 421 LEU 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 108 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 123 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** 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 = 0.3747 r_free = 0.3747 target = 0.094540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.067162 restraints weight = 41744.087| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.12 r_work: 0.3012 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4572 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= 0.152 Angle : 0.666 12.243 24372 Z= 0.366 Chirality : 0.038 0.231 2769 Planarity : 0.004 0.043 2079 Dihedral : 29.566 177.435 4599 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.14 % Rotamer: Outliers : 1.01 % Allowed : 26.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.25), residues: 1253 helix: 1.82 (0.19), residues: 773 sheet: -1.58 (0.73), residues: 66 loop : -1.66 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.013 0.001 TYR F 51 PHE 0.013 0.001 PHE K 109 TRP 0.072 0.004 TRP K 267 HIS 0.007 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00337 (17114) covalent geometry : angle 0.66621 (24372) hydrogen bonds : bond 0.03816 ( 925) hydrogen bonds : angle 3.15923 ( 2379) ********************** 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 183 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 172 time to evaluate : 0.374 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: 0.8355 (mp0) cc_final: 0.8113 (mp0) REVERT: A 94 GLU cc_start: 0.8340 (tt0) cc_final: 0.7702 (tp30) REVERT: A 105 GLU cc_start: 0.8543 (tt0) cc_final: 0.8338 (tp30) REVERT: C 90 ASP cc_start: 0.8427 (t0) cc_final: 0.8106 (t0) REVERT: C 95 LYS cc_start: 0.9129 (tppp) cc_final: 0.8896 (tppp) REVERT: D 30 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.4859 (tpm170) REVERT: D 59 MET cc_start: 0.9095 (mmm) cc_final: 0.8754 (mmt) REVERT: E 73 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8536 (tm-30) REVERT: F 79 LYS cc_start: 0.9288 (ttmm) cc_final: 0.9009 (ttmm) REVERT: G 73 ASN cc_start: 0.9067 (t0) cc_final: 0.8550 (t0) REVERT: H 48 ASP cc_start: 0.9155 (p0) cc_final: 0.8730 (p0) REVERT: K 91 LEU cc_start: 0.8813 (mp) cc_final: 0.8410 (pp) REVERT: K 109 PHE cc_start: 0.8411 (m-10) cc_final: 0.7858 (m-80) REVERT: K 223 MET cc_start: 0.8671 (tmm) cc_final: 0.8429 (tmm) REVERT: K 266 ARG cc_start: 0.9072 (ptm-80) cc_final: 0.8667 (ptm-80) REVERT: K 385 PHE cc_start: 0.8087 (m-80) cc_final: 0.7051 (m-80) REVERT: K 493 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8188 (t) outliers start: 11 outliers final: 8 residues processed: 179 average time/residue: 0.6997 time to fit residues: 136.0574 Evaluate side-chains 176 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 421 LEU 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 61 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.091865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.064284 restraints weight = 42150.533| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.08 r_work: 0.2967 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17114 Z= 0.260 Angle : 0.719 12.097 24372 Z= 0.395 Chirality : 0.041 0.222 2769 Planarity : 0.004 0.046 2079 Dihedral : 29.862 177.378 4599 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 1.56 % Allowed : 26.03 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.25), residues: 1253 helix: 1.59 (0.19), residues: 779 sheet: -1.63 (0.71), residues: 71 loop : -1.79 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 99 TYR 0.014 0.002 TYR K 545 PHE 0.014 0.002 PHE K 119 TRP 0.057 0.004 TRP K 267 HIS 0.007 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00603 (17114) covalent geometry : angle 0.71883 (24372) hydrogen bonds : bond 0.04709 ( 925) hydrogen bonds : angle 3.45555 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4611.26 seconds wall clock time: 79 minutes 17.70 seconds (4757.70 seconds total)