Starting phenix.real_space_refine on Wed Feb 12 12:05:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cia_45615/02_2025/9cia_45615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cia_45615/02_2025/9cia_45615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cia_45615/02_2025/9cia_45615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cia_45615/02_2025/9cia_45615.map" model { file = "/net/cci-nas-00/data/ceres_data/9cia_45615/02_2025/9cia_45615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cia_45615/02_2025/9cia_45615.cif" } resolution = 3.39 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5089 2.51 5 N 1280 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7918 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 772 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "b" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "e" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 975 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "f" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "m" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 278 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "n" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 295 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "d" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 647 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "g" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 811 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.21, per 1000 atoms: 0.66 Number of scatterers: 7918 At special positions: 0 Unit cell: (72.16, 130.38, 141.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1496 8.00 N 1280 7.00 C 5089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.03 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.03 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 16 sheets defined 25.7% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.626A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 41 through 43 No H-bonds generated for 'chain 'D' and resid 41 through 43' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'a' and resid 30 through 55 removed outlier: 3.734A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE a 55 " --> pdb=" O LEU a 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 54 removed outlier: 3.623A pdb=" N LYS b 54 " --> pdb=" O PHE b 50 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 155 removed outlier: 3.638A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 108 removed outlier: 3.573A pdb=" N ALA f 108 " --> pdb=" O PRO f 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 155 Processing helix chain 'm' and resid 239 through 272 removed outlier: 3.959A pdb=" N MET m 244 " --> pdb=" O GLU m 240 " (cutoff:3.500A) Processing helix chain 'n' and resid 242 through 276 removed outlier: 3.779A pdb=" N TYR n 253 " --> pdb=" O THR n 249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU n 256 " --> pdb=" O TYR n 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 124 removed outlier: 3.679A pdb=" N ILE d 113 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 Processing helix chain 'g' and resid 111 through 135 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 24 removed outlier: 3.548A pdb=" N ILE A 22 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.738A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 87 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 103 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.719A pdb=" N MET B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.062A pdb=" N LEU B 45 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 93 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 13 removed outlier: 3.799A pdb=" N GLN C 90 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN C 35 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.580A pdb=" N ILE C 76 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 71 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 17 through 23 removed outlier: 3.568A pdb=" N ASP D 73 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.401A pdb=" N LEU D 45 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL D 111 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.401A pdb=" N LEU D 45 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 92 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR D 116 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'e' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'e' and resid 64 through 66 removed outlier: 4.311A pdb=" N TRP e 59 " --> pdb=" O ILE e 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR e 111 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS d 89 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR e 113 " --> pdb=" O HIS d 89 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ARG d 91 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG e 115 " --> pdb=" O ARG d 91 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY d 69 " --> pdb=" O VAL d 88 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG d 72 " --> pdb=" O TRP d 43 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP d 43 " --> pdb=" O ARG d 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 38 through 41 Processing sheet with id=AB5, first strand: chain 'f' and resid 64 through 66 removed outlier: 3.606A pdb=" N ILE f 66 " --> pdb=" O TRP f 59 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TRP f 59 " --> pdb=" O ILE f 66 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR f 111 " --> pdb=" O GLN g 98 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR g 100 " --> pdb=" O TYR f 111 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ARG g 102 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 122 through 124 Processing sheet with id=AB7, first strand: chain 'd' and resid 26 through 29 removed outlier: 3.974A pdb=" N GLY d 61 " --> pdb=" O VAL d 33 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL d 35 " --> pdb=" O ASP d 59 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP d 59 " --> pdb=" O VAL d 35 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2456 1.35 - 1.47: 2055 1.47 - 1.59: 3497 1.59 - 1.71: 0 1.71 - 1.83: 75 Bond restraints: 8083 Sorted by residual: bond pdb=" N ARG C 31 " pdb=" CA ARG C 31 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.54e-02 4.22e+03 2.20e+00 bond pdb=" CG LEU e 112 " pdb=" CD1 LEU e 112 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.15e+00 bond pdb=" C GLU e 120 " pdb=" N ASN e 121 " ideal model delta sigma weight residual 1.328 1.347 -0.019 1.30e-02 5.92e+03 2.11e+00 bond pdb=" CB VAL C 45 " pdb=" CG2 VAL C 45 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.06e+00 bond pdb=" CA ASN e 121 " pdb=" CB ASN e 121 " ideal model delta sigma weight residual 1.527 1.550 -0.023 1.61e-02 3.86e+03 1.96e+00 ... (remaining 8078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 10730 2.34 - 4.69: 206 4.69 - 7.03: 31 7.03 - 9.38: 4 9.38 - 11.72: 2 Bond angle restraints: 10973 Sorted by residual: angle pdb=" C GLU e 120 " pdb=" N ASN e 121 " pdb=" CA ASN e 121 " ideal model delta sigma weight residual 122.82 129.94 -7.12 1.42e+00 4.96e-01 2.52e+01 angle pdb=" C LYS g 79 " pdb=" N ASP g 80 " pdb=" CA ASP g 80 " ideal model delta sigma weight residual 121.80 133.07 -11.27 2.44e+00 1.68e-01 2.13e+01 angle pdb=" C TYR C 51 " pdb=" N THR C 52 " pdb=" CA THR C 52 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ILE C 30 " pdb=" N ARG C 31 " pdb=" CA ARG C 31 " ideal model delta sigma weight residual 122.46 128.05 -5.59 1.41e+00 5.03e-01 1.57e+01 angle pdb=" CA CYS D 22 " pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " ideal model delta sigma weight residual 114.40 122.79 -8.39 2.30e+00 1.89e-01 1.33e+01 ... (remaining 10968 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4355 17.31 - 34.61: 372 34.61 - 51.92: 82 51.92 - 69.23: 11 69.23 - 86.54: 3 Dihedral angle restraints: 4823 sinusoidal: 1856 harmonic: 2967 Sorted by residual: dihedral pdb=" CB CYS e 49 " pdb=" SG CYS e 49 " pdb=" SG CYS e 98 " pdb=" CB CYS e 98 " ideal model delta sinusoidal sigma weight residual 93.00 50.31 42.69 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA ASN e 121 " pdb=" C ASN e 121 " pdb=" N CYS e 122 " pdb=" CA CYS e 122 " ideal model delta harmonic sigma weight residual 180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA CYS f 119 " pdb=" C CYS f 119 " pdb=" N GLU f 120 " pdb=" CA GLU f 120 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 4820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1054 0.064 - 0.127: 188 0.127 - 0.191: 14 0.191 - 0.254: 3 0.254 - 0.318: 1 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CB ILE d 24 " pdb=" CA ILE d 24 " pdb=" CG1 ILE d 24 " pdb=" CG2 ILE d 24 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL d 88 " pdb=" CA VAL d 88 " pdb=" CG1 VAL d 88 " pdb=" CG2 VAL d 88 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ASP g 80 " pdb=" N ASP g 80 " pdb=" C ASP g 80 " pdb=" CB ASP g 80 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1257 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 59 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO C 60 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 40 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO A 41 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 41 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 41 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 40 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO C 41 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.029 5.00e-02 4.00e+02 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1879 2.79 - 3.32: 6943 3.32 - 3.85: 13250 3.85 - 4.37: 14800 4.37 - 4.90: 26120 Nonbonded interactions: 62992 Sorted by model distance: nonbonded pdb=" OD1 ASP A 83 " pdb=" OH TYR A 87 " model vdw 2.263 3.040 nonbonded pdb=" OG SER e 93 " pdb=" O LEU e 114 " model vdw 2.280 3.040 nonbonded pdb=" O GLN f 92 " pdb=" OH TYR f 96 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 99 " pdb=" O SER B 105 " model vdw 2.321 3.040 nonbonded pdb=" O THR C 9 " pdb=" OG1 THR C 103 " model vdw 2.327 3.040 ... (remaining 62987 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' selection = (chain 'C' and (resid 2 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 24 or (resid 25 through 29 \ and (name N or name CA or name C or name O or name CB )) or resid 30 through 53 \ or (resid 54 through 55 and (name N or name CA or name C or name O or name CB )) \ or resid 56 through 58 or (resid 59 and (name N or name CA or name C or name O \ or name CB )) or resid 60 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 or (resid 78 and (name N or name CA or na \ me C or name O or name CB )) or resid 79 through 105)) } ncs_group { reference = (chain 'B' and (resid 1 through 109 or (resid 110 and (name N or name CA or name \ C or name O or name CB )) or resid 111 through 120)) selection = (chain 'D' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 through 19 or (resid 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 82 or (resid 83 and (na \ me N or name CA or name C or name O or name CB )) or resid 84 through 115 or (re \ sid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 th \ rough 120)) } ncs_group { reference = chain 'a' selection = (chain 'b' and (resid 27 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or (resid 70 through 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 through 88 or (resid 89 through \ 91 and (name N or name CA or name C or name O or name CB )) or resid 92 through \ 155)) selection = chain 'f' } 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.410 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 : 0.004 0.048 8083 Z= 0.252 Angle : 0.799 11.723 10973 Z= 0.420 Chirality : 0.048 0.318 1260 Planarity : 0.005 0.055 1356 Dihedral : 13.152 86.536 2892 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.12 % Allowed : 3.89 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.25), residues: 995 helix: -0.15 (0.31), residues: 229 sheet: -1.49 (0.31), residues: 276 loop : -1.29 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP f 151 HIS 0.003 0.001 HIS m 238 PHE 0.019 0.002 PHE b 40 TYR 0.020 0.002 TYR e 36 ARG 0.003 0.000 ARG f 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7712 (tt0) cc_final: 0.6935 (tt0) REVERT: A 68 SER cc_start: 0.7801 (t) cc_final: 0.7115 (p) REVERT: C 46 LYS cc_start: 0.8618 (ptmm) cc_final: 0.8402 (ptpp) REVERT: D 30 THR cc_start: 0.6775 (t) cc_final: 0.6523 (m) REVERT: D 34 MET cc_start: 0.7669 (tpp) cc_final: 0.7321 (mmt) REVERT: e 40 ILE cc_start: 0.8391 (mm) cc_final: 0.8104 (mm) REVERT: f 39 SER cc_start: 0.8150 (t) cc_final: 0.7852 (m) REVERT: n 276 ARG cc_start: 0.6170 (tmm160) cc_final: 0.5848 (tpp80) REVERT: d 58 LEU cc_start: 0.6274 (tp) cc_final: 0.5974 (tt) REVERT: d 98 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7391 (tt0) REVERT: g 32 LYS cc_start: 0.7988 (mmpt) cc_final: 0.7343 (tttm) REVERT: g 34 TYR cc_start: 0.6100 (t80) cc_final: 0.5895 (t80) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1987 time to fit residues: 67.6475 Evaluate side-chains 208 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 GLN e 60 GLN f 61 HIS f 62 ASN ** f 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.213538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.185762 restraints weight = 11225.371| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.65 r_work: 0.4343 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8083 Z= 0.192 Angle : 0.594 6.647 10973 Z= 0.308 Chirality : 0.041 0.170 1260 Planarity : 0.004 0.046 1356 Dihedral : 5.084 28.390 1166 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.36 % Allowed : 14.15 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.27), residues: 995 helix: 1.39 (0.33), residues: 233 sheet: -1.09 (0.31), residues: 284 loop : -1.12 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 97 HIS 0.001 0.000 HIS m 238 PHE 0.013 0.001 PHE d 125 TYR 0.021 0.002 TYR e 99 ARG 0.004 0.000 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7681 (tt0) cc_final: 0.6850 (tt0) REVERT: A 68 SER cc_start: 0.7623 (t) cc_final: 0.7161 (p) REVERT: B 34 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7150 (mtp) REVERT: B 38 LYS cc_start: 0.7526 (tttt) cc_final: 0.7063 (ttmt) REVERT: B 80 TYR cc_start: 0.8097 (m-80) cc_final: 0.7809 (m-10) REVERT: C 83 ASP cc_start: 0.8295 (t0) cc_final: 0.8092 (t0) REVERT: C 97 TRP cc_start: 0.7922 (m-10) cc_final: 0.7312 (m-10) REVERT: D 34 MET cc_start: 0.7678 (tpp) cc_final: 0.7283 (mmt) REVERT: D 80 TYR cc_start: 0.8366 (m-10) cc_final: 0.8114 (m-10) REVERT: e 106 GLU cc_start: 0.7418 (mp0) cc_final: 0.7150 (mp0) REVERT: f 83 SER cc_start: 0.8683 (m) cc_final: 0.8192 (p) REVERT: n 276 ARG cc_start: 0.6165 (tmm160) cc_final: 0.5957 (ttm-80) REVERT: d 87 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7820 (tm-30) REVERT: d 98 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7364 (tt0) REVERT: g 32 LYS cc_start: 0.7987 (mmpt) cc_final: 0.7442 (tttm) REVERT: g 34 TYR cc_start: 0.6091 (t80) cc_final: 0.5859 (t80) outliers start: 20 outliers final: 14 residues processed: 242 average time/residue: 0.1803 time to fit residues: 60.1617 Evaluate side-chains 227 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain e residue 33 GLN Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain d residue 34 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 GLN ** f 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 248 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.209654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.181102 restraints weight = 11512.201| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 2.72 r_work: 0.4309 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8083 Z= 0.204 Angle : 0.587 7.870 10973 Z= 0.301 Chirality : 0.041 0.157 1260 Planarity : 0.004 0.043 1356 Dihedral : 4.919 23.893 1166 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.89 % Allowed : 18.40 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 995 helix: 1.97 (0.34), residues: 233 sheet: -0.80 (0.32), residues: 272 loop : -1.11 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP f 151 HIS 0.010 0.001 HIS f 61 PHE 0.013 0.001 PHE d 125 TYR 0.021 0.002 TYR b 42 ARG 0.003 0.000 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7063 (mtp) REVERT: B 38 LYS cc_start: 0.7493 (tttt) cc_final: 0.7180 (ttpp) REVERT: B 107 TRP cc_start: 0.6707 (p-90) cc_final: 0.6418 (p-90) REVERT: C 83 ASP cc_start: 0.8458 (t0) cc_final: 0.8203 (t0) REVERT: D 80 TYR cc_start: 0.8333 (m-10) cc_final: 0.8087 (m-10) REVERT: e 106 GLU cc_start: 0.7434 (mp0) cc_final: 0.7220 (mp0) REVERT: f 61 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8053 (t70) REVERT: f 83 SER cc_start: 0.8759 (m) cc_final: 0.8241 (p) REVERT: d 87 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7778 (tm-30) REVERT: d 98 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7318 (tt0) REVERT: g 32 LYS cc_start: 0.8026 (mmpt) cc_final: 0.7421 (tttm) outliers start: 33 outliers final: 27 residues processed: 230 average time/residue: 0.1808 time to fit residues: 56.9687 Evaluate side-chains 226 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain e residue 33 GLN Chi-restraints excluded: chain e residue 56 GLU Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 61 HIS Chi-restraints excluded: chain f residue 106 GLU Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 108 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 93 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 89 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN C 38 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 GLN ** f 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.203881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.173180 restraints weight = 11376.516| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.81 r_work: 0.4179 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8083 Z= 0.291 Angle : 0.639 8.813 10973 Z= 0.326 Chirality : 0.042 0.168 1260 Planarity : 0.004 0.043 1356 Dihedral : 5.024 21.633 1166 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.90 % Allowed : 18.75 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.27), residues: 995 helix: 1.91 (0.33), residues: 233 sheet: -0.97 (0.32), residues: 273 loop : -1.13 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP f 151 HIS 0.015 0.002 HIS f 61 PHE 0.012 0.002 PHE d 125 TYR 0.020 0.002 TYR b 42 ARG 0.004 0.001 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7227 (mm-40) REVERT: A 95 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 34 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7142 (mtp) REVERT: C 83 ASP cc_start: 0.8532 (t0) cc_final: 0.8107 (t0) REVERT: C 97 TRP cc_start: 0.8146 (m-10) cc_final: 0.7660 (m-10) REVERT: D 6 GLN cc_start: 0.8339 (mt0) cc_final: 0.8081 (mt0) REVERT: D 43 LYS cc_start: 0.6792 (tptm) cc_final: 0.6470 (mmmt) REVERT: D 80 TYR cc_start: 0.8491 (m-10) cc_final: 0.8270 (m-10) REVERT: f 78 ASP cc_start: 0.8314 (t0) cc_final: 0.8010 (t0) REVERT: f 79 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: f 83 SER cc_start: 0.8849 (m) cc_final: 0.8337 (p) REVERT: f 125 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6417 (mtp) REVERT: n 256 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7900 (tt) REVERT: d 98 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7419 (tt0) REVERT: g 32 LYS cc_start: 0.8032 (mmpt) cc_final: 0.7395 (tttp) outliers start: 50 outliers final: 35 residues processed: 234 average time/residue: 0.1744 time to fit residues: 56.9409 Evaluate side-chains 238 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain e residue 33 GLN Chi-restraints excluded: chain e residue 93 SER Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 79 GLU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 106 GLU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 GLN ** f 92 GLN ** 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 = 0.4620 r_free = 0.4620 target = 0.204937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.174710 restraints weight = 11293.387| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.78 r_work: 0.4201 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8083 Z= 0.245 Angle : 0.605 7.581 10973 Z= 0.309 Chirality : 0.041 0.170 1260 Planarity : 0.003 0.042 1356 Dihedral : 4.962 22.654 1166 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.90 % Allowed : 21.11 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.27), residues: 995 helix: 2.03 (0.33), residues: 233 sheet: -0.79 (0.32), residues: 265 loop : -1.19 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP f 151 HIS 0.012 0.001 HIS f 61 PHE 0.013 0.002 PHE f 87 TYR 0.018 0.002 TYR b 42 ARG 0.003 0.000 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 203 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8545 (tt) REVERT: C 83 ASP cc_start: 0.8538 (t0) cc_final: 0.8120 (t0) REVERT: D 6 GLN cc_start: 0.8273 (mt0) cc_final: 0.7949 (mt0) REVERT: D 80 TYR cc_start: 0.8466 (m-10) cc_final: 0.8235 (m-10) REVERT: e 33 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: e 75 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.6876 (mt) REVERT: e 106 GLU cc_start: 0.7499 (mp0) cc_final: 0.7250 (mp0) REVERT: f 78 ASP cc_start: 0.8319 (t0) cc_final: 0.8073 (t0) REVERT: f 83 SER cc_start: 0.8818 (m) cc_final: 0.8295 (p) REVERT: f 125 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.6348 (mtp) REVERT: n 256 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7881 (tt) REVERT: d 87 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7783 (tm-30) REVERT: d 98 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7391 (tt0) REVERT: g 32 LYS cc_start: 0.8012 (mmpt) cc_final: 0.7387 (tttp) REVERT: g 34 TYR cc_start: 0.6221 (t80) cc_final: 0.6002 (t80) outliers start: 50 outliers final: 36 residues processed: 229 average time/residue: 0.1631 time to fit residues: 52.8565 Evaluate side-chains 237 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain e residue 33 GLN Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain g residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 36 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.206736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.176832 restraints weight = 11309.809| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.79 r_work: 0.4230 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8083 Z= 0.198 Angle : 0.588 6.841 10973 Z= 0.299 Chirality : 0.041 0.170 1260 Planarity : 0.003 0.040 1356 Dihedral : 4.872 31.927 1166 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.54 % Allowed : 21.82 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.39 (0.27), residues: 995 helix: 2.18 (0.33), residues: 233 sheet: -0.68 (0.32), residues: 260 loop : -1.21 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP f 151 HIS 0.010 0.001 HIS f 61 PHE 0.011 0.001 PHE f 87 TYR 0.017 0.001 TYR b 42 ARG 0.003 0.000 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 ASP cc_start: 0.8600 (t0) cc_final: 0.8193 (t0) REVERT: D 6 GLN cc_start: 0.8169 (mt0) cc_final: 0.7856 (mt0) REVERT: D 80 TYR cc_start: 0.8381 (m-10) cc_final: 0.8164 (m-10) REVERT: e 75 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.6847 (mt) REVERT: e 106 GLU cc_start: 0.7477 (mp0) cc_final: 0.7254 (mp0) REVERT: f 83 SER cc_start: 0.8798 (m) cc_final: 0.8272 (p) REVERT: f 125 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6134 (mtp) REVERT: m 255 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8214 (mp) REVERT: n 256 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7876 (tt) REVERT: g 32 LYS cc_start: 0.7969 (mmpt) cc_final: 0.7371 (tttp) REVERT: g 34 TYR cc_start: 0.6126 (t80) cc_final: 0.5919 (t80) outliers start: 47 outliers final: 34 residues processed: 227 average time/residue: 0.1654 time to fit residues: 53.1719 Evaluate side-chains 230 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain m residue 238 HIS Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 GLN m 263 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.204174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.173862 restraints weight = 11470.254| |-----------------------------------------------------------------------------| r_work (start): 0.4339 rms_B_bonded: 2.81 r_work: 0.4178 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8083 Z= 0.263 Angle : 0.634 7.560 10973 Z= 0.324 Chirality : 0.042 0.195 1260 Planarity : 0.003 0.041 1356 Dihedral : 4.918 28.804 1166 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.25 % Allowed : 21.46 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.27), residues: 995 helix: 2.13 (0.33), residues: 233 sheet: -0.76 (0.32), residues: 260 loop : -1.27 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 36 HIS 0.009 0.001 HIS f 61 PHE 0.015 0.002 PHE D 64 TYR 0.017 0.002 TYR b 42 ARG 0.003 0.000 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8562 (tt) REVERT: B 4 LEU cc_start: 0.7691 (mt) cc_final: 0.7095 (tp) REVERT: C 83 ASP cc_start: 0.8652 (t0) cc_final: 0.8329 (t0) REVERT: D 6 GLN cc_start: 0.8259 (mt0) cc_final: 0.7929 (mt0) REVERT: D 13 LYS cc_start: 0.8189 (mmtm) cc_final: 0.7916 (mmtt) REVERT: D 80 TYR cc_start: 0.8458 (m-10) cc_final: 0.8134 (m-10) REVERT: e 75 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.6762 (mt) REVERT: e 106 GLU cc_start: 0.7530 (mp0) cc_final: 0.7298 (mp0) REVERT: f 83 SER cc_start: 0.8848 (m) cc_final: 0.8318 (p) REVERT: f 106 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6946 (mm-30) REVERT: f 125 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6263 (mtp) REVERT: m 255 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8199 (mp) REVERT: n 256 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7890 (tt) REVERT: g 32 LYS cc_start: 0.7974 (mmpt) cc_final: 0.7334 (tttp) REVERT: g 34 TYR cc_start: 0.6266 (t80) cc_final: 0.6049 (t80) outliers start: 53 outliers final: 40 residues processed: 224 average time/residue: 0.1611 time to fit residues: 51.1695 Evaluate side-chains 237 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 106 GLU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain m residue 238 HIS Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain g residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** 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 = 0.4584 r_free = 0.4584 target = 0.201089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.171150 restraints weight = 11540.047| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.72 r_work: 0.4162 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8083 Z= 0.348 Angle : 0.688 7.356 10973 Z= 0.352 Chirality : 0.044 0.188 1260 Planarity : 0.004 0.041 1356 Dihedral : 5.158 27.682 1166 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.49 % Allowed : 21.58 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 995 helix: 2.12 (0.33), residues: 227 sheet: -1.04 (0.32), residues: 255 loop : -1.39 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 36 HIS 0.009 0.001 HIS f 61 PHE 0.019 0.002 PHE f 87 TYR 0.020 0.002 TYR D 32 ARG 0.004 0.001 ARG g 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8586 (tt) REVERT: C 83 ASP cc_start: 0.8686 (t0) cc_final: 0.8415 (t0) REVERT: C 97 TRP cc_start: 0.8196 (m-10) cc_final: 0.7256 (m-10) REVERT: D 6 GLN cc_start: 0.8299 (mt0) cc_final: 0.8029 (mt0) REVERT: D 13 LYS cc_start: 0.8249 (mmtm) cc_final: 0.8030 (mmtt) REVERT: D 43 LYS cc_start: 0.6835 (tptm) cc_final: 0.6556 (tptp) REVERT: D 80 TYR cc_start: 0.8507 (m-10) cc_final: 0.8172 (m-10) REVERT: e 75 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.6824 (mt) REVERT: f 83 SER cc_start: 0.8850 (m) cc_final: 0.8319 (p) REVERT: f 125 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6286 (mtp) REVERT: f 155 ARG cc_start: 0.7537 (mpt-90) cc_final: 0.5172 (ttt90) REVERT: n 256 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8014 (tt) REVERT: d 23 LYS cc_start: 0.6348 (pttm) cc_final: 0.5765 (tptp) REVERT: g 32 LYS cc_start: 0.7982 (mmpt) cc_final: 0.7434 (tttp) outliers start: 55 outliers final: 43 residues processed: 228 average time/residue: 0.1758 time to fit residues: 56.2426 Evaluate side-chains 243 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain m residue 238 HIS Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain g residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 5 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** 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 = 0.4623 r_free = 0.4623 target = 0.205680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.175707 restraints weight = 11547.325| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 2.82 r_work: 0.4207 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8083 Z= 0.212 Angle : 0.630 9.594 10973 Z= 0.319 Chirality : 0.042 0.228 1260 Planarity : 0.003 0.040 1356 Dihedral : 4.887 25.862 1166 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.42 % Allowed : 22.88 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.27), residues: 995 helix: 2.18 (0.33), residues: 233 sheet: -0.89 (0.32), residues: 252 loop : -1.32 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 36 HIS 0.010 0.001 HIS f 61 PHE 0.012 0.001 PHE f 87 TYR 0.016 0.002 TYR e 149 ARG 0.003 0.000 ARG e 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.7088 (tttt) cc_final: 0.6795 (ttpp) REVERT: C 83 ASP cc_start: 0.8632 (t0) cc_final: 0.8389 (t0) REVERT: C 97 TRP cc_start: 0.8013 (m-10) cc_final: 0.7214 (m-10) REVERT: D 6 GLN cc_start: 0.8147 (mt0) cc_final: 0.7883 (mt0) REVERT: D 43 LYS cc_start: 0.6788 (tptm) cc_final: 0.6432 (tptp) REVERT: D 80 TYR cc_start: 0.8392 (m-10) cc_final: 0.8084 (m-10) REVERT: e 75 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.6715 (mt) REVERT: e 106 GLU cc_start: 0.7460 (mp0) cc_final: 0.7242 (mp0) REVERT: f 83 SER cc_start: 0.8768 (m) cc_final: 0.8255 (p) REVERT: f 125 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6163 (mtp) REVERT: f 155 ARG cc_start: 0.7435 (mpt-90) cc_final: 0.5168 (ttt90) REVERT: n 245 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7537 (tt0) REVERT: n 256 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7893 (tt) REVERT: g 32 LYS cc_start: 0.7921 (mmpt) cc_final: 0.7315 (tttm) REVERT: g 34 TYR cc_start: 0.6211 (t80) cc_final: 0.5972 (t80) outliers start: 46 outliers final: 39 residues processed: 220 average time/residue: 0.1777 time to fit residues: 54.3773 Evaluate side-chains 229 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain a residue 47 THR Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 145 LEU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 110 PHE Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain m residue 238 HIS Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 GLN C 38 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.198325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.167944 restraints weight = 11547.506| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 2.71 r_work: 0.4103 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 8083 Z= 0.552 Angle : 0.844 10.383 10973 Z= 0.432 Chirality : 0.049 0.249 1260 Planarity : 0.005 0.045 1356 Dihedral : 5.675 26.776 1166 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.31 % Allowed : 23.94 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 995 helix: 1.52 (0.32), residues: 226 sheet: -1.43 (0.31), residues: 264 loop : -1.59 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 36 HIS 0.008 0.002 HIS f 61 PHE 0.030 0.003 PHE f 87 TYR 0.026 0.003 TYR n 255 ARG 0.006 0.001 ARG g 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1990 Ramachandran restraints generated. 995 Oldfield, 0 Emsley, 995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 ASP cc_start: 0.8621 (t0) cc_final: 0.8236 (t0) REVERT: C 97 TRP cc_start: 0.8237 (m-10) cc_final: 0.7669 (m-10) REVERT: D 19 LYS cc_start: 0.8119 (tppt) cc_final: 0.7864 (tppt) REVERT: D 43 LYS cc_start: 0.6968 (tptm) cc_final: 0.6682 (mmmt) REVERT: D 80 TYR cc_start: 0.8605 (m-10) cc_final: 0.8354 (m-10) REVERT: e 75 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.6854 (mt) REVERT: f 83 SER cc_start: 0.8908 (m) cc_final: 0.8359 (p) REVERT: f 125 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6545 (mtp) REVERT: f 150 TYR cc_start: 0.7031 (t80) cc_final: 0.6763 (t80) REVERT: f 155 ARG cc_start: 0.7586 (mpt-90) cc_final: 0.5266 (ttt90) REVERT: n 256 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8199 (tt) REVERT: d 23 LYS cc_start: 0.6375 (pttm) cc_final: 0.5767 (tptp) REVERT: g 32 LYS cc_start: 0.8035 (mmpt) cc_final: 0.7466 (tttp) outliers start: 45 outliers final: 41 residues processed: 232 average time/residue: 0.1850 time to fit residues: 58.9948 Evaluate side-chains 247 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 203 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 46 LEU Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain e residue 46 ILE Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 122 CYS Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 34 THR Chi-restraints excluded: chain f residue 45 VAL Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 110 PHE Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 127 VAL Chi-restraints excluded: chain f residue 134 VAL Chi-restraints excluded: chain m residue 238 HIS Chi-restraints excluded: chain m residue 260 VAL Chi-restraints excluded: chain n residue 256 LEU Chi-restraints excluded: chain d residue 34 PHE Chi-restraints excluded: chain d residue 94 GLN Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 103 THR Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.208033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.179824 restraints weight = 11512.608| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.61 r_work: 0.4253 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8083 Z= 0.234 Angle : 0.668 10.141 10973 Z= 0.339 Chirality : 0.043 0.213 1260 Planarity : 0.004 0.041 1356 Dihedral : 5.172 24.985 1166 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.48 % Allowed : 25.71 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 995 helix: 1.95 (0.33), residues: 233 sheet: -1.12 (0.32), residues: 253 loop : -1.48 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 36 HIS 0.010 0.001 HIS f 61 PHE 0.013 0.001 PHE f 87 TYR 0.020 0.002 TYR n 255 ARG 0.003 0.000 ARG e 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.06 seconds wall clock time: 67 minutes 57.40 seconds (4077.40 seconds total)