Starting phenix.real_space_refine on Tue Sep 24 10:53:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cia_45615/09_2024/9cia_45615.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cia_45615/09_2024/9cia_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cia_45615/09_2024/9cia_45615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cia_45615/09_2024/9cia_45615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cia_45615/09_2024/9cia_45615.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cia_45615/09_2024/9cia_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.11, per 1000 atoms: 0.77 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: 1.65 Conformation dependent library (CDL) restraints added in 963.9 milliseconds 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: 0.86 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: 2.02 Time building geometry restraints manager: 1.99 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.940 Find NCS groups from input model: 0.230 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:2.880 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 0.921 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: 0.1876 time to fit residues: 64.3794 Evaluate side-chains 208 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7750 (tt0) cc_final: 0.6819 (tt0) REVERT: A 68 SER cc_start: 0.7796 (t) cc_final: 0.7293 (p) REVERT: B 34 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7272 (mtp) REVERT: B 38 LYS cc_start: 0.7439 (tttt) cc_final: 0.6897 (ttmt) REVERT: B 80 TYR cc_start: 0.8127 (m-80) cc_final: 0.7837 (m-10) REVERT: C 46 LYS cc_start: 0.8635 (ptmm) cc_final: 0.8383 (ptpp) REVERT: C 83 ASP cc_start: 0.8279 (t0) cc_final: 0.8070 (t0) REVERT: C 97 TRP cc_start: 0.7966 (m-10) cc_final: 0.7399 (m-10) REVERT: D 34 MET cc_start: 0.7673 (tpp) cc_final: 0.7266 (mmt) REVERT: D 80 TYR cc_start: 0.8372 (m-10) cc_final: 0.8109 (m-10) REVERT: e 106 GLU cc_start: 0.7436 (mp0) cc_final: 0.7151 (mp0) REVERT: e 120 GLU cc_start: 0.7754 (tp30) cc_final: 0.7552 (tp30) REVERT: f 83 SER cc_start: 0.8759 (m) cc_final: 0.8212 (p) REVERT: n 276 ARG cc_start: 0.6180 (tmm160) cc_final: 0.5903 (ttm-80) REVERT: d 87 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7773 (tm-30) REVERT: d 98 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7343 (tt0) REVERT: g 32 LYS cc_start: 0.7994 (mmpt) cc_final: 0.7339 (tttm) REVERT: g 34 TYR cc_start: 0.6203 (t80) cc_final: 0.5958 (t80) outliers start: 20 outliers final: 14 residues processed: 242 average time/residue: 0.1887 time to fit residues: 63.0168 Evaluate side-chains 227 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 48 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ** f 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 8083 Z= 0.460 Angle : 0.753 8.988 10973 Z= 0.387 Chirality : 0.046 0.157 1260 Planarity : 0.005 0.048 1356 Dihedral : 5.666 26.623 1166 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 6.01 % Allowed : 18.04 % Favored : 75.94 % 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: -1.11 (0.27), residues: 995 helix: 1.29 (0.33), residues: 232 sheet: -1.42 (0.31), residues: 292 loop : -1.26 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 36 HIS 0.009 0.002 HIS f 61 PHE 0.020 0.003 PHE f 87 TYR 0.025 0.003 TYR b 42 ARG 0.007 0.001 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 266 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 215 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7968 (tt0) cc_final: 0.7123 (tt0) REVERT: A 95 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8590 (tt) REVERT: B 34 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7445 (mtp) REVERT: B 106 ASP cc_start: 0.7263 (p0) cc_final: 0.6829 (p0) REVERT: C 46 LYS cc_start: 0.8719 (ptmm) cc_final: 0.8508 (ptpp) REVERT: C 54 ARG cc_start: 0.6644 (ptt-90) cc_final: 0.6437 (mpp80) REVERT: C 83 ASP cc_start: 0.8532 (t0) cc_final: 0.8170 (t0) REVERT: D 6 GLN cc_start: 0.8523 (mt0) cc_final: 0.8271 (mt0) REVERT: D 13 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7819 (mmtt) REVERT: D 43 LYS cc_start: 0.6889 (tptm) cc_final: 0.6660 (mmmm) REVERT: D 80 TYR cc_start: 0.8535 (m-10) cc_final: 0.8253 (m-10) REVERT: e 75 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.6885 (mt) REVERT: e 120 GLU cc_start: 0.7982 (tp30) cc_final: 0.7781 (tp30) REVERT: f 61 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.8154 (t-90) REVERT: f 78 ASP cc_start: 0.8526 (t0) cc_final: 0.8237 (t0) REVERT: f 83 SER cc_start: 0.8930 (m) cc_final: 0.8353 (p) REVERT: f 125 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6396 (mtp) REVERT: n 256 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8086 (tt) REVERT: n 276 ARG cc_start: 0.6141 (tmm160) cc_final: 0.5721 (ttm-80) REVERT: d 98 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7423 (tt0) REVERT: g 32 LYS cc_start: 0.8052 (mmpt) cc_final: 0.7417 (tttp) outliers start: 51 outliers final: 39 residues processed: 241 average time/residue: 0.1742 time to fit residues: 57.8504 Evaluate side-chains 245 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 200 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR 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 30 ILE Chi-restraints excluded: chain C residue 34 LEU 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 41 HIS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 69 THR 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 44 THR Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 93 SER 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 61 HIS Chi-restraints excluded: chain f residue 106 GLU 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 95 LYS Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 126 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 35 ASN B 6 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** 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 f 60 GLN ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 ASN ** f 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8083 Z= 0.189 Angle : 0.588 7.911 10973 Z= 0.301 Chirality : 0.041 0.182 1260 Planarity : 0.003 0.041 1356 Dihedral : 5.076 21.463 1166 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.36 % Allowed : 21.82 % Favored : 73.82 % 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: -0.59 (0.27), residues: 995 helix: 1.95 (0.33), residues: 233 sheet: -0.89 (0.32), residues: 270 loop : -1.25 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP f 151 HIS 0.013 0.001 HIS f 61 PHE 0.019 0.001 PHE m 264 TYR 0.020 0.002 TYR b 42 ARG 0.003 0.000 ARG e 117 *********************** 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 251 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 214 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7253 (mtp) REVERT: C 46 LYS cc_start: 0.8747 (ptmm) cc_final: 0.8506 (ptpp) REVERT: C 83 ASP cc_start: 0.8516 (t0) cc_final: 0.8094 (t0) REVERT: D 6 GLN cc_start: 0.8384 (mt0) cc_final: 0.8071 (mt0) REVERT: D 80 TYR cc_start: 0.8330 (m-10) cc_final: 0.8063 (m-10) REVERT: e 106 GLU cc_start: 0.7491 (mp0) cc_final: 0.7243 (mp0) REVERT: e 119 CYS cc_start: 0.4913 (OUTLIER) cc_final: 0.4654 (p) REVERT: e 120 GLU cc_start: 0.7859 (tp30) cc_final: 0.7613 (tp30) REVERT: f 78 ASP cc_start: 0.8387 (t0) cc_final: 0.8149 (t0) REVERT: f 83 SER cc_start: 0.8830 (m) cc_final: 0.8255 (p) REVERT: n 276 ARG cc_start: 0.6286 (tmm160) cc_final: 0.5884 (ttm-80) REVERT: d 87 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7663 (tm-30) REVERT: d 98 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7363 (tt0) REVERT: g 32 LYS cc_start: 0.7947 (mmpt) cc_final: 0.7258 (tttp) outliers start: 37 outliers final: 23 residues processed: 234 average time/residue: 0.1806 time to fit residues: 58.9668 Evaluate side-chains 225 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 200 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 37 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 b residue 44 VAL Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 145 LEU 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 127 VAL 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 Chi-restraints excluded: chain g residue 95 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.0170 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 23 optimal weight: 30.0000 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN e 33 GLN ** f 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8083 Z= 0.205 Angle : 0.596 9.419 10973 Z= 0.303 Chirality : 0.041 0.165 1260 Planarity : 0.003 0.041 1356 Dihedral : 4.924 22.880 1166 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.31 % Allowed : 21.82 % Favored : 72.88 % 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: -0.41 (0.27), residues: 995 helix: 2.14 (0.33), residues: 233 sheet: -0.67 (0.33), residues: 264 loop : -1.23 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 36 HIS 0.011 0.001 HIS f 61 PHE 0.016 0.001 PHE m 264 TYR 0.019 0.002 TYR b 42 ARG 0.003 0.000 ARG e 117 *********************** 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 246 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 201 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8503 (tt) REVERT: C 46 LYS cc_start: 0.8736 (ptmm) cc_final: 0.8495 (ptpp) REVERT: C 83 ASP cc_start: 0.8523 (t0) cc_final: 0.8130 (t0) REVERT: D 6 GLN cc_start: 0.8296 (mt0) cc_final: 0.7997 (mt0) REVERT: D 80 TYR cc_start: 0.8321 (m-10) cc_final: 0.8057 (m-10) REVERT: e 106 GLU cc_start: 0.7486 (mp0) cc_final: 0.7232 (mp0) REVERT: e 120 GLU cc_start: 0.7835 (tp30) cc_final: 0.7547 (tp30) REVERT: f 78 ASP cc_start: 0.8436 (t0) cc_final: 0.8197 (t0) REVERT: f 83 SER cc_start: 0.8863 (m) cc_final: 0.8294 (p) REVERT: f 106 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: f 125 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6351 (mtp) REVERT: n 276 ARG cc_start: 0.6259 (tmm160) cc_final: 0.5910 (ttm-80) REVERT: d 98 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7313 (tt0) REVERT: g 32 LYS cc_start: 0.7905 (mmpt) cc_final: 0.7273 (tttp) REVERT: g 34 TYR cc_start: 0.6296 (t80) cc_final: 0.6080 (t80) outliers start: 45 outliers final: 32 residues processed: 226 average time/residue: 0.1728 time to fit residues: 54.6818 Evaluate side-chains 231 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 MET 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 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 93 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 7 optimal weight: 9.9990 chunk 49 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8083 Z= 0.176 Angle : 0.592 12.661 10973 Z= 0.298 Chirality : 0.041 0.181 1260 Planarity : 0.003 0.040 1356 Dihedral : 4.796 32.810 1166 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.60 % Allowed : 22.64 % Favored : 72.76 % 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: -0.29 (0.27), residues: 995 helix: 2.32 (0.33), residues: 233 sheet: -0.58 (0.33), residues: 265 loop : -1.22 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 36 HIS 0.009 0.001 HIS f 61 PHE 0.014 0.001 PHE m 264 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 243 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 37 TYR cc_start: 0.8197 (m-80) cc_final: 0.7981 (m-80) REVERT: C 46 LYS cc_start: 0.8769 (ptmm) cc_final: 0.8522 (ptpp) REVERT: C 83 ASP cc_start: 0.8535 (t0) cc_final: 0.8166 (t0) REVERT: D 80 TYR cc_start: 0.8268 (m-10) cc_final: 0.8039 (m-10) REVERT: e 75 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.6698 (mt) REVERT: e 106 GLU cc_start: 0.7442 (mp0) cc_final: 0.7196 (mp0) REVERT: f 83 SER cc_start: 0.8841 (m) cc_final: 0.8268 (p) REVERT: f 106 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: f 125 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6209 (mtp) REVERT: n 256 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7968 (tp) REVERT: n 276 ARG cc_start: 0.6176 (tmm160) cc_final: 0.5927 (ttm-80) REVERT: d 87 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7647 (tm-30) REVERT: g 32 LYS cc_start: 0.7894 (mmpt) cc_final: 0.7205 (tttm) REVERT: g 34 TYR cc_start: 0.6172 (t80) cc_final: 0.5936 (t80) outliers start: 39 outliers final: 27 residues processed: 224 average time/residue: 0.1705 time to fit residues: 52.9260 Evaluate side-chains 222 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 e residue 75 ILE 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 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 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** 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 51 GLN ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8083 Z= 0.277 Angle : 0.650 11.223 10973 Z= 0.331 Chirality : 0.043 0.174 1260 Planarity : 0.004 0.040 1356 Dihedral : 4.921 28.143 1166 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 5.90 % Allowed : 21.82 % 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: -0.52 (0.27), residues: 995 helix: 2.09 (0.33), residues: 233 sheet: -0.84 (0.32), residues: 279 loop : -1.25 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 36 HIS 0.009 0.001 HIS f 61 PHE 0.014 0.002 PHE f 87 TYR 0.018 0.002 TYR b 42 ARG 0.003 0.000 ARG C 54 *********************** 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 250 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 200 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8537 (tt) REVERT: B 106 ASP cc_start: 0.6744 (p0) cc_final: 0.6522 (p0) REVERT: C 37 TYR cc_start: 0.8301 (m-80) cc_final: 0.8061 (m-80) REVERT: C 46 LYS cc_start: 0.8780 (ptmm) cc_final: 0.8524 (ptpp) REVERT: C 83 ASP cc_start: 0.8587 (t0) cc_final: 0.8162 (t0) REVERT: C 97 TRP cc_start: 0.8232 (m-10) cc_final: 0.7749 (m-10) REVERT: D 6 GLN cc_start: 0.8297 (mt0) cc_final: 0.7996 (mt0) REVERT: D 13 LYS cc_start: 0.8237 (mmtm) cc_final: 0.7987 (mmtt) REVERT: D 80 TYR cc_start: 0.8405 (m-10) cc_final: 0.8085 (m-10) REVERT: b 40 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7067 (t80) REVERT: e 75 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.6806 (mt) REVERT: e 106 GLU cc_start: 0.7482 (mp0) cc_final: 0.7216 (mp0) REVERT: f 83 SER cc_start: 0.8905 (m) cc_final: 0.8331 (p) REVERT: f 106 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6928 (mm-30) REVERT: f 125 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6315 (mtp) REVERT: f 155 ARG cc_start: 0.7398 (mpt-90) cc_final: 0.5038 (ttt90) REVERT: m 255 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8153 (mp) REVERT: n 256 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7922 (tt) REVERT: n 276 ARG cc_start: 0.6291 (tmm160) cc_final: 0.5852 (ttm-80) REVERT: d 87 GLN cc_start: 0.8251 (tm-30) cc_final: 0.7474 (tm-30) REVERT: g 32 LYS cc_start: 0.7911 (mmpt) cc_final: 0.7288 (tttp) outliers start: 50 outliers final: 35 residues processed: 225 average time/residue: 0.1927 time to fit residues: 60.9352 Evaluate side-chains 237 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 81 MET 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 48 MET 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 40 PHE Chi-restraints excluded: chain b residue 44 VAL Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 125 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8083 Z= 0.211 Angle : 0.625 16.155 10973 Z= 0.311 Chirality : 0.042 0.168 1260 Planarity : 0.003 0.040 1356 Dihedral : 4.769 26.912 1166 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.42 % Allowed : 23.70 % Favored : 70.87 % 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: -0.43 (0.27), residues: 995 helix: 2.18 (0.33), residues: 233 sheet: -0.72 (0.32), residues: 263 loop : -1.25 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 36 HIS 0.010 0.001 HIS f 61 PHE 0.011 0.001 PHE m 264 TYR 0.016 0.002 TYR b 42 ARG 0.003 0.000 ARG e 117 *********************** 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 248 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 38 LYS cc_start: 0.7023 (tttt) cc_final: 0.6715 (ttpp) REVERT: B 39 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.5943 (tt0) REVERT: C 37 TYR cc_start: 0.8238 (m-80) cc_final: 0.7980 (m-80) REVERT: C 46 LYS cc_start: 0.8799 (ptmm) cc_final: 0.8541 (ptpp) REVERT: C 83 ASP cc_start: 0.8590 (t0) cc_final: 0.8261 (t0) REVERT: C 97 TRP cc_start: 0.8190 (m-10) cc_final: 0.7717 (m-10) REVERT: D 13 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7894 (mmtt) REVERT: D 80 TYR cc_start: 0.8352 (m-10) cc_final: 0.8087 (m-10) REVERT: b 40 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7011 (t80) REVERT: e 75 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.6643 (mt) REVERT: e 106 GLU cc_start: 0.7474 (mp0) cc_final: 0.7222 (mp0) REVERT: f 83 SER cc_start: 0.8880 (m) cc_final: 0.8299 (p) REVERT: f 123 MET cc_start: 0.7783 (ptm) cc_final: 0.7549 (ptm) REVERT: f 125 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.6221 (mtp) REVERT: f 155 ARG cc_start: 0.7388 (mpt-90) cc_final: 0.5172 (ttt90) REVERT: m 255 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8179 (mp) REVERT: n 245 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7528 (tt0) REVERT: n 256 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7901 (tt) REVERT: n 276 ARG cc_start: 0.6102 (tmm160) cc_final: 0.5896 (ttm-80) REVERT: d 87 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7589 (tm-30) REVERT: g 32 LYS cc_start: 0.7865 (mmpt) cc_final: 0.7186 (tttm) REVERT: g 34 TYR cc_start: 0.6281 (t80) cc_final: 0.6044 (t80) outliers start: 46 outliers final: 33 residues processed: 227 average time/residue: 0.1813 time to fit residues: 56.2833 Evaluate side-chains 236 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 81 MET 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 48 MET 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 40 PHE Chi-restraints excluded: chain e residue 75 ILE 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 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 108 ILE Chi-restraints excluded: chain d residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN ** f 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8083 Z= 0.310 Angle : 0.685 15.036 10973 Z= 0.345 Chirality : 0.044 0.207 1260 Planarity : 0.004 0.041 1356 Dihedral : 5.025 26.336 1166 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 5.78 % Allowed : 23.00 % Favored : 71.23 % 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: -0.61 (0.27), residues: 995 helix: 2.21 (0.33), residues: 227 sheet: -0.94 (0.31), residues: 279 loop : -1.34 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 36 HIS 0.010 0.001 HIS f 61 PHE 0.015 0.002 PHE f 87 TYR 0.018 0.002 TYR D 32 ARG 0.004 0.000 ARG g 102 *********************** 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 247 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8614 (tt) REVERT: B 38 LYS cc_start: 0.6941 (tttt) cc_final: 0.6692 (ttpp) REVERT: B 39 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.5950 (tt0) REVERT: B 106 ASP cc_start: 0.6803 (p0) cc_final: 0.6594 (p0) REVERT: C 37 TYR cc_start: 0.8327 (m-80) cc_final: 0.8024 (m-80) REVERT: C 83 ASP cc_start: 0.8618 (t0) cc_final: 0.8331 (t0) REVERT: D 6 GLN cc_start: 0.8299 (mt0) cc_final: 0.8005 (mt0) REVERT: D 13 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7850 (mmtt) REVERT: D 80 TYR cc_start: 0.8528 (m-10) cc_final: 0.8174 (m-10) REVERT: b 40 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7063 (t80) REVERT: e 75 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.6762 (mt) REVERT: e 106 GLU cc_start: 0.7483 (mp0) cc_final: 0.7214 (mp0) REVERT: f 83 SER cc_start: 0.8936 (m) cc_final: 0.8352 (p) REVERT: f 125 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6380 (mtp) REVERT: f 155 ARG cc_start: 0.7401 (mpt-90) cc_final: 0.5203 (ttt90) REVERT: m 255 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8145 (mp) REVERT: n 256 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7971 (tt) REVERT: n 276 ARG cc_start: 0.6171 (tmm160) cc_final: 0.5828 (ttm-80) REVERT: d 87 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7588 (tm-30) REVERT: g 32 LYS cc_start: 0.7930 (mmpt) cc_final: 0.7323 (tttp) outliers start: 49 outliers final: 38 residues processed: 222 average time/residue: 0.1771 time to fit residues: 54.2121 Evaluate side-chains 242 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 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 95 LEU Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 87 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 98 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 48 MET 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 40 PHE Chi-restraints excluded: chain e residue 46 ILE Chi-restraints excluded: chain e residue 75 ILE 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 94 GLN Chi-restraints excluded: chain d residue 96 CYS Chi-restraints excluded: chain d residue 108 ILE Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain g residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8083 Z= 0.186 Angle : 0.630 15.009 10973 Z= 0.313 Chirality : 0.042 0.189 1260 Planarity : 0.003 0.040 1356 Dihedral : 4.748 25.127 1166 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.07 % Allowed : 23.82 % Favored : 71.11 % 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: -0.44 (0.27), residues: 995 helix: 2.22 (0.33), residues: 233 sheet: -0.81 (0.32), residues: 274 loop : -1.23 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 36 HIS 0.011 0.001 HIS f 61 PHE 0.010 0.001 PHE d 34 TYR 0.018 0.001 TYR e 149 ARG 0.004 0.000 ARG e 117 ********************** 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 245 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 202 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 LYS cc_start: 0.6891 (tttt) cc_final: 0.6654 (ttpp) REVERT: B 39 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.5913 (tt0) REVERT: C 83 ASP cc_start: 0.8599 (t0) cc_final: 0.8332 (t0) REVERT: D 13 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7793 (mmtt) REVERT: D 80 TYR cc_start: 0.8393 (m-10) cc_final: 0.8133 (m-10) REVERT: b 40 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7071 (t80) REVERT: e 75 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.6640 (mt) REVERT: e 106 GLU cc_start: 0.7434 (mp0) cc_final: 0.7209 (mp0) REVERT: f 83 SER cc_start: 0.8825 (m) cc_final: 0.8260 (p) REVERT: f 155 ARG cc_start: 0.7426 (mpt-90) cc_final: 0.5346 (ttt90) REVERT: n 245 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7435 (tt0) REVERT: n 256 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7946 (tt) REVERT: d 87 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7683 (tm-30) REVERT: g 32 LYS cc_start: 0.7854 (mmpt) cc_final: 0.7191 (tttm) REVERT: g 34 TYR cc_start: 0.6182 (t80) cc_final: 0.5962 (t80) outliers start: 43 outliers final: 34 residues processed: 225 average time/residue: 0.1834 time to fit residues: 57.6868 Evaluate side-chains 232 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain B residue 39 GLN 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 37 VAL Chi-restraints excluded: chain D residue 48 MET 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 40 PHE Chi-restraints excluded: chain e residue 75 ILE 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 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 108 ILE Chi-restraints excluded: chain d residue 109 VAL Chi-restraints excluded: chain g residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.203054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.173554 restraints weight = 11385.146| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.72 r_work: 0.4201 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8083 Z= 0.288 Angle : 0.685 14.679 10973 Z= 0.341 Chirality : 0.044 0.192 1260 Planarity : 0.004 0.041 1356 Dihedral : 4.869 25.661 1166 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.19 % Allowed : 24.06 % 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: -0.52 (0.27), residues: 995 helix: 2.26 (0.33), residues: 227 sheet: -0.87 (0.32), residues: 271 loop : -1.29 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 36 HIS 0.010 0.001 HIS f 61 PHE 0.013 0.002 PHE f 87 TYR 0.017 0.002 TYR b 42 ARG 0.004 0.001 ARG C 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2175.22 seconds wall clock time: 39 minutes 27.63 seconds (2367.63 seconds total)