Starting phenix.real_space_refine on Fri Jul 25 22:02:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqp_61732/07_2025/9jqp_61732_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqp_61732/07_2025/9jqp_61732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jqp_61732/07_2025/9jqp_61732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqp_61732/07_2025/9jqp_61732.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqp_61732/07_2025/9jqp_61732_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqp_61732/07_2025/9jqp_61732_neut.cif" } resolution = 3.34 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= -0.036 sd= 0.244 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 37 5.16 5 C 5164 2.51 5 N 1377 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8175 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1474 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 185} Chain breaks: 4 Chain: "B" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1608 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "E" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1604 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Chain: "H" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 873 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "I" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 97} Chain breaks: 1 Chain: "J" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 890 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "K" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.75, per 1000 atoms: 0.83 Number of scatterers: 8175 At special positions: 0 Unit cell: (98.8, 138.7, 99.75, 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 37 16.00 O 1597 8.00 N 1377 7.00 C 5164 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 93 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 86 " " NAG B 401 " - " ASN B 86 " " NAG E 601 " - " ASN E 18 " " NAG E 602 " - " ASN E 86 " " NAG E 603 " - " ASN E 92 " " NAG E 604 " - " ASN E 194 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 971.1 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 25 sheets defined 3.2% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'B' and resid 72 through 75 removed outlier: 3.788A pdb=" N ILE B 75 " --> pdb=" O ARG B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.679A pdb=" N ARG E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.776A pdb=" N SER H 76 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.714A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 5.578A pdb=" N ILE A 11 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA A 115 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ALA A 13 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 93 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 129 removed outlier: 6.681A pdb=" N HIS A 134 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A 128 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLY A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 179 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 151 removed outlier: 8.927A pdb=" N VAL B 123 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER A 205 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL B 125 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER A 207 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR B 140 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL B 175 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 151 removed outlier: 8.927A pdb=" N VAL B 123 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER A 205 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N VAL B 125 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER A 207 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 133 " --> pdb=" O MET B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 14 removed outlier: 4.040A pdb=" N LYS B 37 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 100 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 147 through 151 removed outlier: 3.840A pdb=" N SER B 190 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 200 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.873A pdb=" N ALA E 81 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.358A pdb=" N ILE E 11 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA E 115 " --> pdb=" O ILE E 11 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA E 13 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE E 39 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.814A pdb=" N LEU E 122 " --> pdb=" O ILE E 138 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE E 138 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 124 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 136 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 188 through 194 removed outlier: 3.987A pdb=" N ILE E 193 " --> pdb=" O LYS E 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB6, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.686A pdb=" N LEU H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 33 through 34 removed outlier: 3.750A pdb=" N TYR H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG H 99 " --> pdb=" O TYR H 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 58 through 60 removed outlier: 4.791A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR H 111 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'I' and resid 50 through 54 removed outlier: 6.057A pdb=" N LEU I 51 " --> pdb=" O VAL I 42 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL I 42 " --> pdb=" O LEU I 51 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE I 53 " --> pdb=" O TRP I 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.515A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.656A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU J 34 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR J 33 " --> pdb=" O ARG J 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.745A pdb=" N ASP K 75 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'K' and resid 50 through 53 removed outlier: 6.509A pdb=" N TRP K 40 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL K 90 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 50 through 53 removed outlier: 6.509A pdb=" N TRP K 40 " --> pdb=" O LEU K 52 " (cutoff:3.500A) 202 hydrogen bonds defined for protein. 477 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: 2.00 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1630 1.33 - 1.45: 2112 1.45 - 1.57: 4546 1.57 - 1.69: 0 1.69 - 1.82: 54 Bond restraints: 8342 Sorted by residual: bond pdb=" CA LYS E 51 " pdb=" C LYS E 51 " ideal model delta sigma weight residual 1.520 1.465 0.056 1.21e-02 6.83e+03 2.13e+01 bond pdb=" CA TYR K 54 " pdb=" C TYR K 54 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.33e-02 5.65e+03 9.27e+00 bond pdb=" CA GLU E 35 " pdb=" C GLU E 35 " ideal model delta sigma weight residual 1.526 1.483 0.043 1.42e-02 4.96e+03 9.22e+00 bond pdb=" CA GLN K 18 " pdb=" C GLN K 18 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.23e-02 6.61e+03 8.69e+00 bond pdb=" C LYS K 55 " pdb=" N VAL K 56 " ideal model delta sigma weight residual 1.335 1.302 0.033 1.20e-02 6.94e+03 7.72e+00 ... (remaining 8337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 10775 1.90 - 3.80: 423 3.80 - 5.71: 61 5.71 - 7.61: 32 7.61 - 9.51: 5 Bond angle restraints: 11296 Sorted by residual: angle pdb=" N THR E 8 " pdb=" CA THR E 8 " pdb=" C THR E 8 " ideal model delta sigma weight residual 111.14 118.09 -6.95 1.08e+00 8.57e-01 4.14e+01 angle pdb=" C SER A 185 " pdb=" CA SER A 185 " pdb=" CB SER A 185 " ideal model delta sigma weight residual 116.54 109.31 7.23 1.15e+00 7.56e-01 3.95e+01 angle pdb=" N VAL A 46 " pdb=" CA VAL A 46 " pdb=" C VAL A 46 " ideal model delta sigma weight residual 108.53 117.10 -8.57 1.45e+00 4.76e-01 3.49e+01 angle pdb=" N GLU J 50 " pdb=" CA GLU J 50 " pdb=" C GLU J 50 " ideal model delta sigma weight residual 109.07 116.46 -7.39 1.52e+00 4.33e-01 2.36e+01 angle pdb=" N ALA J 12 " pdb=" CA ALA J 12 " pdb=" C ALA J 12 " ideal model delta sigma weight residual 108.60 115.67 -7.07 1.46e+00 4.69e-01 2.35e+01 ... (remaining 11291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 4350 17.24 - 34.49: 535 34.49 - 51.73: 117 51.73 - 68.97: 28 68.97 - 86.22: 7 Dihedral angle restraints: 5037 sinusoidal: 2051 harmonic: 2986 Sorted by residual: dihedral pdb=" CB CYS A 23 " pdb=" SG CYS A 23 " pdb=" SG CYS A 97 " pdb=" CB CYS A 97 " ideal model delta sinusoidal sigma weight residual -86.00 -153.83 67.83 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS E 137 " pdb=" SG CYS E 137 " pdb=" SG CYS E 191 " pdb=" CB CYS E 191 " ideal model delta sinusoidal sigma weight residual 93.00 158.27 -65.27 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 97 " pdb=" CB CYS B 97 " ideal model delta sinusoidal sigma weight residual 93.00 152.29 -59.29 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 5034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1082 0.073 - 0.146: 183 0.146 - 0.219: 3 0.219 - 0.292: 2 0.292 - 0.365: 1 Chirality restraints: 1271 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 18 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 86 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 86 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1268 not shown) Planarity restraints: 1439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.280 2.00e-02 2.50e+03 2.35e-01 6.93e+02 pdb=" C7 NAG A 601 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.401 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 601 " 0.233 2.00e-02 2.50e+03 1.93e-01 4.65e+02 pdb=" C7 NAG E 601 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG E 601 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG E 601 " -0.317 2.00e-02 2.50e+03 pdb=" O7 NAG E 601 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 51 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LEU K 51 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU K 51 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU K 52 " -0.014 2.00e-02 2.50e+03 ... (remaining 1436 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 144 2.62 - 3.19: 6898 3.19 - 3.76: 11307 3.76 - 4.33: 15758 4.33 - 4.90: 27052 Nonbonded interactions: 61159 Sorted by model distance: nonbonded pdb=" OE1 GLN H 43 " pdb=" O GLY H 44 " model vdw 2.056 3.040 nonbonded pdb=" O ILE B 75 " pdb=" OG1 THR B 76 " model vdw 2.172 3.040 nonbonded pdb=" OG SER H 91 " pdb=" O LEU H 113 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN A 152 " pdb=" N ASN A 153 " model vdw 2.221 3.120 nonbonded pdb=" O GLU H 10 " pdb=" OG1 THR H 114 " model vdw 2.221 3.040 ... (remaining 61154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 119 or resid 121 through 123 or resid 125 throug \ h 128 or resid 130 through 152 or resid 154 through 159 or resid 161 through 173 \ or resid 175 through 183 or resid 185 through 191 or resid 193 through 194 or r \ esid 196 through 213 or resid 601)) selection = (chain 'B' and (resid 3 through 25 or resid 32 through 50 or resid 52 through 71 \ or resid 80 through 102 or resid 104 through 119 or resid 121 through 123 or re \ sid 125 through 128 or resid 130 through 152 or resid 154 through 159 or resid 1 \ 61 through 173 or resid 175 through 183 or resid 185 through 191 or resid 193 th \ rough 194 or resid 196 through 213 or resid 401)) } ncs_group { reference = chain 'H' selection = (chain 'J' and (resid 2 through 54 or resid 57 through 115)) } ncs_group { reference = chain 'I' selection = (chain 'K' and (resid 1 through 63 or resid 70 through 109)) } 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: 7.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.000 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.006 0.056 8358 Z= 0.362 Angle : 0.893 9.509 11334 Z= 0.522 Chirality : 0.050 0.365 1271 Planarity : 0.009 0.235 1433 Dihedral : 15.529 86.217 3109 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.25 % Allowed : 29.02 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -2.39 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -1.32 (0.23), residues: 489 loop : -1.80 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 47 HIS 0.005 0.001 HIS A 134 PHE 0.022 0.002 PHE J 29 TYR 0.037 0.002 TYR B 105 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 6) link_NAG-ASN : angle 3.76544 ( 18) hydrogen bonds : bond 0.19305 ( 183) hydrogen bonds : angle 7.22279 ( 477) SS BOND : bond 0.00292 ( 10) SS BOND : angle 0.87439 ( 20) covalent geometry : bond 0.00572 ( 8342) covalent geometry : angle 0.88108 (11296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7783 (t0) cc_final: 0.7555 (t0) REVERT: A 133 ILE cc_start: 0.8884 (mm) cc_final: 0.8560 (mm) REVERT: A 180 ILE cc_start: 0.8439 (mt) cc_final: 0.8121 (mt) REVERT: A 213 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6453 (m-10) REVERT: B 203 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8477 (p) REVERT: E 90 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7282 (tm-30) REVERT: E 189 MET cc_start: 0.6682 (tpt) cc_final: 0.6392 (tpt) REVERT: J 91 SER cc_start: 0.8431 (m) cc_final: 0.8094 (p) outliers start: 11 outliers final: 5 residues processed: 263 average time/residue: 0.2657 time to fit residues: 88.2231 Evaluate side-chains 237 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 230 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 57 ASN Chi-restraints excluded: chain K residue 79 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 39 GLN J 43 GLN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.062828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052010 restraints weight = 24073.667| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.46 r_work: 0.2661 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8358 Z= 0.141 Angle : 0.668 7.355 11334 Z= 0.343 Chirality : 0.046 0.187 1271 Planarity : 0.004 0.042 1433 Dihedral : 5.667 52.672 1276 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.42 % Allowed : 28.91 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.89 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.95 (0.23), residues: 484 loop : -1.50 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 38 HIS 0.006 0.001 HIS J 3 PHE 0.012 0.001 PHE E 39 TYR 0.021 0.002 TYR H 80 ARG 0.007 0.001 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 6) link_NAG-ASN : angle 2.92186 ( 18) hydrogen bonds : bond 0.03729 ( 183) hydrogen bonds : angle 5.73234 ( 477) SS BOND : bond 0.00571 ( 10) SS BOND : angle 0.91683 ( 20) covalent geometry : bond 0.00324 ( 8342) covalent geometry : angle 0.65809 (11296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7373 (m-90) cc_final: 0.6840 (m-90) REVERT: A 55 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7441 (mt-10) REVERT: A 91 ASP cc_start: 0.8810 (m-30) cc_final: 0.8596 (m-30) REVERT: A 124 ASP cc_start: 0.8035 (t0) cc_final: 0.7749 (t0) REVERT: A 153 ASN cc_start: 0.8298 (t0) cc_final: 0.8031 (t0) REVERT: B 104 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: B 130 ASP cc_start: 0.8453 (t0) cc_final: 0.7824 (t0) REVERT: B 200 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8899 (mp) REVERT: B 203 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8903 (p) REVERT: E 125 MET cc_start: 0.9093 (mtm) cc_final: 0.8853 (mtm) REVERT: E 189 MET cc_start: 0.8166 (tpt) cc_final: 0.7641 (tpt) REVERT: J 90 ASP cc_start: 0.8953 (t0) cc_final: 0.8745 (t0) outliers start: 39 outliers final: 22 residues processed: 256 average time/residue: 0.2394 time to fit residues: 79.3616 Evaluate side-chains 234 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 93 CYS Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 57 ASN Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN K 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.049696 restraints weight = 24677.784| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.46 r_work: 0.2602 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8358 Z= 0.178 Angle : 0.691 8.320 11334 Z= 0.361 Chirality : 0.047 0.185 1271 Planarity : 0.004 0.041 1433 Dihedral : 6.009 55.762 1274 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.67 % Allowed : 27.78 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.85 (0.25), residues: 1022 helix: None (None), residues: 0 sheet: -0.72 (0.23), residues: 467 loop : -1.68 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 38 HIS 0.007 0.002 HIS J 3 PHE 0.024 0.002 PHE E 207 TYR 0.021 0.002 TYR H 80 ARG 0.004 0.001 ARG I 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 6) link_NAG-ASN : angle 3.23213 ( 18) hydrogen bonds : bond 0.04020 ( 183) hydrogen bonds : angle 5.83849 ( 477) SS BOND : bond 0.00548 ( 10) SS BOND : angle 1.14523 ( 20) covalent geometry : bond 0.00413 ( 8342) covalent geometry : angle 0.67844 (11296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8782 (t0) cc_final: 0.8085 (t0) REVERT: A 55 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7173 (mt-10) REVERT: A 153 ASN cc_start: 0.8275 (t0) cc_final: 0.8073 (t0) REVERT: B 130 ASP cc_start: 0.8463 (t0) cc_final: 0.8193 (t0) REVERT: B 182 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7622 (mmm160) REVERT: B 203 THR cc_start: 0.9159 (OUTLIER) cc_final: 0.8938 (p) REVERT: E 125 MET cc_start: 0.9059 (mtm) cc_final: 0.8850 (mtm) REVERT: H 81 MET cc_start: 0.9213 (ttp) cc_final: 0.8975 (ttp) REVERT: I 86 GLU cc_start: 0.7929 (pt0) cc_final: 0.7679 (pt0) REVERT: J 90 ASP cc_start: 0.8987 (t0) cc_final: 0.8645 (t0) REVERT: K 87 ASP cc_start: 0.8803 (t0) cc_final: 0.8230 (t0) outliers start: 50 outliers final: 33 residues processed: 260 average time/residue: 0.2385 time to fit residues: 79.6978 Evaluate side-chains 248 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 57 ASN Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.059962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.049290 restraints weight = 24545.913| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.42 r_work: 0.2592 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8358 Z= 0.177 Angle : 0.679 8.615 11334 Z= 0.354 Chirality : 0.046 0.197 1271 Planarity : 0.004 0.055 1433 Dihedral : 5.817 53.836 1274 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.01 % Allowed : 27.89 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.67 (0.25), residues: 1022 helix: None (None), residues: 0 sheet: -0.50 (0.24), residues: 465 loop : -1.66 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 47 HIS 0.008 0.002 HIS J 3 PHE 0.024 0.002 PHE A 104 TYR 0.020 0.002 TYR H 80 ARG 0.004 0.001 ARG E 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 6) link_NAG-ASN : angle 3.19684 ( 18) hydrogen bonds : bond 0.03852 ( 183) hydrogen bonds : angle 5.76589 ( 477) SS BOND : bond 0.00531 ( 10) SS BOND : angle 1.34577 ( 20) covalent geometry : bond 0.00412 ( 8342) covalent geometry : angle 0.66602 (11296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8780 (t0) cc_final: 0.8388 (t0) REVERT: A 55 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7422 (mt-10) REVERT: A 154 LYS cc_start: 0.8735 (pttm) cc_final: 0.8494 (pttm) REVERT: A 156 GLU cc_start: 0.8400 (mp0) cc_final: 0.8178 (mp0) REVERT: B 130 ASP cc_start: 0.8573 (t0) cc_final: 0.8333 (t0) REVERT: B 182 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7801 (mmm160) REVERT: B 203 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8991 (p) REVERT: E 189 MET cc_start: 0.8148 (tpt) cc_final: 0.7674 (tpt) REVERT: H 63 LYS cc_start: 0.9296 (ptpp) cc_final: 0.9010 (mtmm) REVERT: I 74 THR cc_start: 0.8791 (p) cc_final: 0.8521 (p) REVERT: I 86 GLU cc_start: 0.8094 (pt0) cc_final: 0.7890 (pt0) REVERT: K 79 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8795 (tppt) REVERT: K 87 ASP cc_start: 0.8778 (t0) cc_final: 0.8308 (t0) outliers start: 53 outliers final: 39 residues processed: 254 average time/residue: 0.2319 time to fit residues: 76.5944 Evaluate side-chains 249 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 43 GLN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 12 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 HIS J 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.048475 restraints weight = 24553.119| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 2.45 r_work: 0.2563 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 8358 Z= 0.203 Angle : 0.712 9.090 11334 Z= 0.370 Chirality : 0.047 0.210 1271 Planarity : 0.005 0.047 1433 Dihedral : 5.888 53.532 1271 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.35 % Allowed : 28.46 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.61 (0.25), residues: 1022 helix: None (None), residues: 0 sheet: -0.40 (0.24), residues: 469 loop : -1.68 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 47 HIS 0.005 0.002 HIS E 24 PHE 0.025 0.002 PHE A 104 TYR 0.023 0.002 TYR H 33 ARG 0.004 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 6) link_NAG-ASN : angle 3.40327 ( 18) hydrogen bonds : bond 0.04044 ( 183) hydrogen bonds : angle 5.86188 ( 477) SS BOND : bond 0.00625 ( 10) SS BOND : angle 1.27178 ( 20) covalent geometry : bond 0.00474 ( 8342) covalent geometry : angle 0.69765 (11296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.9054 (mm) cc_final: 0.8633 (mm) REVERT: A 154 LYS cc_start: 0.8761 (pttm) cc_final: 0.8533 (pttm) REVERT: A 156 GLU cc_start: 0.8390 (mp0) cc_final: 0.8097 (mp0) REVERT: B 14 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8560 (mtm) REVERT: B 130 ASP cc_start: 0.8651 (t0) cc_final: 0.8309 (t0) REVERT: B 203 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.9000 (p) REVERT: H 63 LYS cc_start: 0.9284 (ptpp) cc_final: 0.9045 (mtmt) REVERT: I 74 THR cc_start: 0.8950 (p) cc_final: 0.8728 (p) REVERT: I 86 GLU cc_start: 0.8185 (pt0) cc_final: 0.7976 (pt0) REVERT: K 79 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8788 (tppt) REVERT: K 87 ASP cc_start: 0.8868 (t0) cc_final: 0.8431 (t0) outliers start: 56 outliers final: 41 residues processed: 256 average time/residue: 0.2340 time to fit residues: 77.7269 Evaluate side-chains 254 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 102 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.0060 chunk 43 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.049123 restraints weight = 24587.032| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.45 r_work: 0.2584 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8358 Z= 0.167 Angle : 0.690 8.628 11334 Z= 0.355 Chirality : 0.046 0.216 1271 Planarity : 0.004 0.040 1433 Dihedral : 5.803 52.502 1271 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 6.35 % Allowed : 27.89 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.47 (0.25), residues: 1022 helix: None (None), residues: 0 sheet: -0.29 (0.24), residues: 469 loop : -1.61 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 36 HIS 0.004 0.001 HIS E 24 PHE 0.023 0.002 PHE A 104 TYR 0.022 0.002 TYR H 33 ARG 0.004 0.000 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00341 ( 6) link_NAG-ASN : angle 3.10764 ( 18) hydrogen bonds : bond 0.03717 ( 183) hydrogen bonds : angle 5.67967 ( 477) SS BOND : bond 0.00587 ( 10) SS BOND : angle 1.40365 ( 20) covalent geometry : bond 0.00388 ( 8342) covalent geometry : angle 0.67731 (11296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.9052 (mm) cc_final: 0.8631 (mm) REVERT: A 154 LYS cc_start: 0.8749 (pttm) cc_final: 0.8527 (pttm) REVERT: A 156 GLU cc_start: 0.8384 (mp0) cc_final: 0.8112 (mp0) REVERT: B 130 ASP cc_start: 0.8607 (t0) cc_final: 0.8292 (t0) REVERT: B 203 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8969 (p) REVERT: E 189 MET cc_start: 0.8214 (tpt) cc_final: 0.7782 (tpt) REVERT: H 63 LYS cc_start: 0.9253 (ptpp) cc_final: 0.9036 (mtmt) REVERT: I 74 THR cc_start: 0.8935 (p) cc_final: 0.8692 (p) REVERT: K 87 ASP cc_start: 0.8868 (t0) cc_final: 0.8499 (t0) outliers start: 56 outliers final: 47 residues processed: 259 average time/residue: 0.2431 time to fit residues: 81.5269 Evaluate side-chains 262 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 214 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 0.0070 chunk 38 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 chunk 94 optimal weight: 0.9980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.060638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.049966 restraints weight = 24614.711| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.45 r_work: 0.2606 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8358 Z= 0.138 Angle : 0.681 8.452 11334 Z= 0.348 Chirality : 0.046 0.223 1271 Planarity : 0.004 0.050 1433 Dihedral : 5.492 51.037 1267 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.10 % Allowed : 30.61 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.35 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.23 (0.24), residues: 471 loop : -1.51 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 38 HIS 0.003 0.001 HIS E 24 PHE 0.023 0.002 PHE A 104 TYR 0.032 0.001 TYR B 105 ARG 0.012 0.001 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 6) link_NAG-ASN : angle 2.76761 ( 18) hydrogen bonds : bond 0.03394 ( 183) hydrogen bonds : angle 5.49612 ( 477) SS BOND : bond 0.00524 ( 10) SS BOND : angle 1.24400 ( 20) covalent geometry : bond 0.00319 ( 8342) covalent geometry : angle 0.67085 (11296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.8376 (mp0) cc_final: 0.8089 (mp0) REVERT: B 14 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8513 (mtm) REVERT: B 130 ASP cc_start: 0.8666 (t0) cc_final: 0.8380 (t0) REVERT: B 203 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8942 (p) REVERT: E 162 LYS cc_start: 0.7581 (ttpp) cc_final: 0.7213 (ptmm) REVERT: E 189 MET cc_start: 0.8232 (tpt) cc_final: 0.7776 (tpt) REVERT: H 63 LYS cc_start: 0.9239 (ptpp) cc_final: 0.9000 (mtmt) REVERT: I 74 THR cc_start: 0.8894 (p) cc_final: 0.8681 (p) REVERT: K 87 ASP cc_start: 0.8873 (t0) cc_final: 0.8479 (t0) outliers start: 45 outliers final: 37 residues processed: 250 average time/residue: 0.2429 time to fit residues: 78.6228 Evaluate side-chains 253 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 GLN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.048411 restraints weight = 24856.920| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 2.47 r_work: 0.2563 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8358 Z= 0.196 Angle : 0.740 8.659 11334 Z= 0.380 Chirality : 0.047 0.238 1271 Planarity : 0.005 0.040 1433 Dihedral : 5.811 49.740 1267 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.90 % Allowed : 29.71 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.35 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.17 (0.24), residues: 477 loop : -1.60 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.004 0.002 HIS B 85 PHE 0.023 0.002 PHE A 104 TYR 0.022 0.002 TYR H 80 ARG 0.004 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 6) link_NAG-ASN : angle 3.19859 ( 18) hydrogen bonds : bond 0.03848 ( 183) hydrogen bonds : angle 5.81678 ( 477) SS BOND : bond 0.00671 ( 10) SS BOND : angle 1.44686 ( 20) covalent geometry : bond 0.00459 ( 8342) covalent geometry : angle 0.72805 (11296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 218 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.9086 (mm) cc_final: 0.8675 (mm) REVERT: A 156 GLU cc_start: 0.8393 (mp0) cc_final: 0.8088 (mp0) REVERT: B 14 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.8534 (mtm) REVERT: B 130 ASP cc_start: 0.8709 (t0) cc_final: 0.8400 (t0) REVERT: B 203 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8972 (p) REVERT: E 77 ARG cc_start: 0.9006 (ttm-80) cc_final: 0.8734 (ttm-80) REVERT: E 162 LYS cc_start: 0.7655 (ttpp) cc_final: 0.7351 (ptmm) REVERT: H 63 LYS cc_start: 0.9223 (ptpp) cc_final: 0.8988 (mtmt) REVERT: I 74 THR cc_start: 0.8976 (p) cc_final: 0.8759 (p) REVERT: K 87 ASP cc_start: 0.8886 (t0) cc_final: 0.8559 (t0) outliers start: 52 outliers final: 45 residues processed: 251 average time/residue: 0.2527 time to fit residues: 82.1312 Evaluate side-chains 259 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 212 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 GLN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 98 optimal weight: 0.0970 chunk 79 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.049216 restraints weight = 25068.865| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.48 r_work: 0.2590 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8358 Z= 0.153 Angle : 0.720 9.455 11334 Z= 0.366 Chirality : 0.047 0.220 1271 Planarity : 0.004 0.040 1433 Dihedral : 5.647 48.832 1267 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.56 % Allowed : 30.27 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.24 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.07 (0.25), residues: 462 loop : -1.50 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 47 HIS 0.004 0.001 HIS E 24 PHE 0.024 0.002 PHE A 104 TYR 0.018 0.001 TYR E 105 ARG 0.007 0.001 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 6) link_NAG-ASN : angle 2.91530 ( 18) hydrogen bonds : bond 0.03505 ( 183) hydrogen bonds : angle 5.65448 ( 477) SS BOND : bond 0.00547 ( 10) SS BOND : angle 1.20809 ( 20) covalent geometry : bond 0.00357 ( 8342) covalent geometry : angle 0.70992 (11296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.9097 (mm) cc_final: 0.8698 (mm) REVERT: A 156 GLU cc_start: 0.8347 (mp0) cc_final: 0.8053 (mp0) REVERT: B 14 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: B 130 ASP cc_start: 0.8695 (t0) cc_final: 0.8400 (t0) REVERT: B 203 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8962 (p) REVERT: E 162 LYS cc_start: 0.7601 (ttpp) cc_final: 0.7355 (ptmm) REVERT: H 63 LYS cc_start: 0.9200 (ptpp) cc_final: 0.8973 (mtmt) REVERT: I 74 THR cc_start: 0.8936 (p) cc_final: 0.8714 (p) REVERT: J 82 GLN cc_start: 0.8984 (mt0) cc_final: 0.8746 (mm-40) REVERT: K 87 ASP cc_start: 0.8906 (t0) cc_final: 0.8650 (t0) outliers start: 49 outliers final: 44 residues processed: 248 average time/residue: 0.2407 time to fit residues: 77.8773 Evaluate side-chains 256 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 210 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 30 ASN Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 90 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.049610 restraints weight = 24540.000| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.47 r_work: 0.2600 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8358 Z= 0.149 Angle : 0.720 10.695 11334 Z= 0.367 Chirality : 0.047 0.247 1271 Planarity : 0.004 0.040 1433 Dihedral : 5.511 47.737 1267 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.33 % Allowed : 31.18 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.15 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.06 (0.25), residues: 469 loop : -1.41 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 47 HIS 0.003 0.001 HIS E 24 PHE 0.024 0.002 PHE A 104 TYR 0.016 0.001 TYR H 80 ARG 0.006 0.001 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 2.79832 ( 18) hydrogen bonds : bond 0.03384 ( 183) hydrogen bonds : angle 5.53494 ( 477) SS BOND : bond 0.00530 ( 10) SS BOND : angle 1.16224 ( 20) covalent geometry : bond 0.00346 ( 8342) covalent geometry : angle 0.71056 (11296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7805 (m-90) cc_final: 0.7525 (m-90) REVERT: A 133 ILE cc_start: 0.9090 (mm) cc_final: 0.8710 (mm) REVERT: A 156 GLU cc_start: 0.8351 (mp0) cc_final: 0.7944 (mp0) REVERT: B 14 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.8515 (mtm) REVERT: B 130 ASP cc_start: 0.8687 (t0) cc_final: 0.8392 (t0) REVERT: B 203 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8950 (p) REVERT: E 90 GLN cc_start: 0.8239 (tm-30) cc_final: 0.8014 (tm-30) REVERT: E 162 LYS cc_start: 0.7604 (ttpp) cc_final: 0.7382 (ptmm) REVERT: H 63 LYS cc_start: 0.9196 (ptpp) cc_final: 0.8972 (mtmt) REVERT: I 74 THR cc_start: 0.8939 (p) cc_final: 0.8714 (p) REVERT: K 87 ASP cc_start: 0.8912 (t0) cc_final: 0.8593 (t0) outliers start: 47 outliers final: 41 residues processed: 245 average time/residue: 0.2365 time to fit residues: 75.6326 Evaluate side-chains 258 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 43 GLN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 115 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 59 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.0020 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.060339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.049573 restraints weight = 24761.916| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.49 r_work: 0.2597 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8358 Z= 0.150 Angle : 0.733 11.231 11334 Z= 0.372 Chirality : 0.047 0.237 1271 Planarity : 0.004 0.040 1433 Dihedral : 5.503 46.619 1267 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.22 % Allowed : 31.86 % Favored : 62.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: -1.10 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.00 (0.25), residues: 469 loop : -1.40 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 47 HIS 0.010 0.001 HIS B 24 PHE 0.024 0.002 PHE A 104 TYR 0.016 0.001 TYR H 80 ARG 0.006 0.001 ARG H 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 6) link_NAG-ASN : angle 2.78352 ( 18) hydrogen bonds : bond 0.03404 ( 183) hydrogen bonds : angle 5.53596 ( 477) SS BOND : bond 0.00518 ( 10) SS BOND : angle 1.15945 ( 20) covalent geometry : bond 0.00351 ( 8342) covalent geometry : angle 0.72367 (11296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4959.72 seconds wall clock time: 86 minutes 16.38 seconds (5176.38 seconds total)