Starting phenix.real_space_refine on Wed Sep 17 10:28:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqp_61732/09_2025/9jqp_61732_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqp_61732/09_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_61732/09_2025/9jqp_61732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqp_61732/09_2025/9jqp_61732.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqp_61732/09_2025/9jqp_61732_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqp_61732/09_2025/9jqp_61732_neut.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.036 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.94, per 1000 atoms: 0.24 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: 0.49 Conformation dependent library (CDL) restraints added in 417.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.20 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: 1.06 Time building geometry restraints manager: 0.69 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 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 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: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.790 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.770 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.000 ARG A 194 TYR 0.037 0.002 TYR B 105 PHE 0.022 0.002 PHE J 29 TRP 0.016 0.001 TRP J 47 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 8342) covalent geometry : angle 0.88108 (11296) SS BOND : bond 0.00292 ( 10) SS BOND : angle 0.87439 ( 20) hydrogen bonds : bond 0.19305 ( 183) hydrogen bonds : angle 7.22279 ( 477) link_NAG-ASN : bond 0.00485 ( 6) link_NAG-ASN : angle 3.76544 ( 18) *********************** 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 : 0.309 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: 0.1158 time to fit residues: 38.6716 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 : 0.257 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3033 r_free = 0.3033 target = 0.062489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.051629 restraints weight = 24357.464| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.47 r_work: 0.2654 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2491 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= 0.147 Angle : 0.675 7.320 11334 Z= 0.346 Chirality : 0.046 0.178 1271 Planarity : 0.004 0.043 1433 Dihedral : 5.729 53.288 1276 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.54 % Allowed : 28.46 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.94 (0.23), residues: 484 loop : -1.51 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 13 TYR 0.022 0.002 TYR H 80 PHE 0.012 0.001 PHE E 39 TRP 0.013 0.001 TRP A 38 HIS 0.006 0.001 HIS J 3 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8342) covalent geometry : angle 0.66443 (11296) SS BOND : bond 0.00583 ( 10) SS BOND : angle 0.91492 ( 20) hydrogen bonds : bond 0.03760 ( 183) hydrogen bonds : angle 5.75407 ( 477) link_NAG-ASN : bond 0.00374 ( 6) link_NAG-ASN : angle 2.98449 ( 18) *********************** 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 271 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8721 (mpp) cc_final: 0.8498 (mpp) REVERT: A 38 TRP cc_start: 0.7410 (m-90) cc_final: 0.6870 (m-90) REVERT: A 55 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7433 (mt-10) REVERT: A 124 ASP cc_start: 0.8048 (t0) cc_final: 0.7754 (t0) REVERT: A 153 ASN cc_start: 0.8304 (t0) cc_final: 0.8040 (t0) REVERT: B 104 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: B 130 ASP cc_start: 0.8475 (t0) cc_final: 0.7829 (t0) REVERT: B 203 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8909 (p) REVERT: E 125 MET cc_start: 0.9100 (mtm) cc_final: 0.8863 (mtm) REVERT: E 136 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8150 (mm-30) REVERT: E 189 MET cc_start: 0.8176 (tpt) cc_final: 0.7653 (tpt) REVERT: J 90 ASP cc_start: 0.8965 (t0) cc_final: 0.8753 (t0) outliers start: 40 outliers final: 23 residues processed: 256 average time/residue: 0.1067 time to fit residues: 35.2600 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 : 0.326 ------------------------------------------------------------------------------- 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 104 PHE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 75 ILE 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 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 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN B 1 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.048967 restraints weight = 24239.117| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 2.43 r_work: 0.2586 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8358 Z= 0.211 Angle : 0.722 8.810 11334 Z= 0.377 Chirality : 0.047 0.194 1271 Planarity : 0.004 0.041 1433 Dihedral : 6.139 55.168 1274 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.01 % Allowed : 27.66 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.25), residues: 1022 helix: None (None), residues: 0 sheet: -0.68 (0.24), residues: 463 loop : -1.67 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 82 TYR 0.023 0.002 TYR H 80 PHE 0.023 0.002 PHE E 207 TRP 0.012 0.002 TRP A 38 HIS 0.007 0.002 HIS J 3 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 8342) covalent geometry : angle 0.70805 (11296) SS BOND : bond 0.00604 ( 10) SS BOND : angle 1.27216 ( 20) hydrogen bonds : bond 0.04265 ( 183) hydrogen bonds : angle 6.00611 ( 477) link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 3.47750 ( 18) *********************** 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 279 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 226 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8753 (t0) cc_final: 0.8381 (t0) REVERT: A 55 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 101 ASP cc_start: 0.7507 (t70) cc_final: 0.7207 (t0) REVERT: A 133 ILE cc_start: 0.9103 (mm) cc_final: 0.8651 (mm) REVERT: A 153 ASN cc_start: 0.8289 (t0) cc_final: 0.8079 (t0) REVERT: B 130 ASP cc_start: 0.8474 (t0) cc_final: 0.8187 (t0) REVERT: B 203 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8933 (p) REVERT: E 54 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8379 (ptm-80) REVERT: H 63 LYS cc_start: 0.9238 (ptpp) cc_final: 0.9023 (ptpp) REVERT: I 43 GLN cc_start: 0.8582 (tt0) cc_final: 0.8362 (tt0) REVERT: J 90 ASP cc_start: 0.8987 (t0) cc_final: 0.8713 (t0) REVERT: K 87 ASP cc_start: 0.8811 (t0) cc_final: 0.8250 (t0) outliers start: 53 outliers final: 35 residues processed: 260 average time/residue: 0.1093 time to fit residues: 36.7409 Evaluate side-chains 250 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 12 LEU 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 54 ARG 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 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 93 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 17 SER 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 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 86 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.050694 restraints weight = 24837.126| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.47 r_work: 0.2629 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8358 Z= 0.126 Angle : 0.638 7.694 11334 Z= 0.330 Chirality : 0.045 0.189 1271 Planarity : 0.004 0.054 1433 Dihedral : 5.631 54.648 1274 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.33 % Allowed : 28.34 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.25), residues: 1022 helix: None (None), residues: 0 sheet: -0.51 (0.24), residues: 471 loop : -1.60 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.017 0.001 TYR H 33 PHE 0.025 0.002 PHE A 104 TRP 0.013 0.001 TRP A 38 HIS 0.009 0.001 HIS J 3 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8342) covalent geometry : angle 0.62844 (11296) SS BOND : bond 0.00448 ( 10) SS BOND : angle 0.95785 ( 20) hydrogen bonds : bond 0.03289 ( 183) hydrogen bonds : angle 5.48416 ( 477) link_NAG-ASN : bond 0.00355 ( 6) link_NAG-ASN : angle 2.70476 ( 18) *********************** 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 269 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8768 (t0) cc_final: 0.8356 (t0) REVERT: A 55 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7300 (mt-10) REVERT: A 101 ASP cc_start: 0.7422 (t70) cc_final: 0.7145 (t0) REVERT: A 153 ASN cc_start: 0.8258 (t0) cc_final: 0.8052 (t0) REVERT: B 104 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: B 130 ASP cc_start: 0.8527 (t0) cc_final: 0.8234 (t0) REVERT: B 203 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8936 (p) REVERT: E 105 TYR cc_start: 0.7659 (p90) cc_final: 0.7452 (p90) REVERT: E 189 MET cc_start: 0.8116 (tpt) cc_final: 0.7667 (tpt) REVERT: H 63 LYS cc_start: 0.9252 (ptpp) cc_final: 0.8934 (mtmt) REVERT: H 81 MET cc_start: 0.9187 (ttp) cc_final: 0.8981 (ttp) REVERT: I 43 GLN cc_start: 0.8564 (tt0) cc_final: 0.8340 (tt0) REVERT: I 74 THR cc_start: 0.8729 (p) cc_final: 0.8437 (p) REVERT: I 86 GLU cc_start: 0.7964 (pt0) cc_final: 0.7747 (pt0) REVERT: I 91 TYR cc_start: 0.7009 (m-10) cc_final: 0.6769 (m-10) REVERT: K 79 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8747 (tppt) REVERT: K 87 ASP cc_start: 0.8823 (t0) cc_final: 0.8321 (t0) outliers start: 47 outliers final: 31 residues processed: 251 average time/residue: 0.1050 time to fit residues: 34.3889 Evaluate side-chains 246 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 203 THR Chi-restraints excluded: chain E residue 55 GLU 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 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 75 SER 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 90 VAL Chi-restraints excluded: chain J residue 17 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.060150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.049365 restraints weight = 24562.697| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.45 r_work: 0.2598 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8358 Z= 0.159 Angle : 0.672 8.350 11334 Z= 0.346 Chirality : 0.046 0.214 1271 Planarity : 0.004 0.042 1433 Dihedral : 5.594 54.267 1272 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.78 % Allowed : 28.80 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.25), residues: 1022 helix: None (None), residues: 0 sheet: -0.36 (0.24), residues: 469 loop : -1.62 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 77 TYR 0.021 0.002 TYR H 33 PHE 0.025 0.002 PHE E 207 TRP 0.011 0.001 TRP A 38 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8342) covalent geometry : angle 0.65938 (11296) SS BOND : bond 0.00469 ( 10) SS BOND : angle 1.31972 ( 20) hydrogen bonds : bond 0.03656 ( 183) hydrogen bonds : angle 5.54417 ( 477) link_NAG-ASN : bond 0.00317 ( 6) link_NAG-ASN : angle 3.02638 ( 18) *********************** 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 272 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.7594 (t70) cc_final: 0.7332 (t0) REVERT: B 130 ASP cc_start: 0.8569 (t0) cc_final: 0.8300 (t0) REVERT: B 203 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8984 (p) REVERT: E 189 MET cc_start: 0.8238 (tpt) cc_final: 0.7736 (tpt) REVERT: H 63 LYS cc_start: 0.9266 (ptpp) cc_final: 0.8985 (mtmt) REVERT: I 74 THR cc_start: 0.8787 (p) cc_final: 0.8552 (p) REVERT: I 86 GLU cc_start: 0.8090 (pt0) cc_final: 0.7880 (pt0) REVERT: K 87 ASP cc_start: 0.8789 (t0) cc_final: 0.8355 (t0) outliers start: 51 outliers final: 38 residues processed: 256 average time/residue: 0.1071 time to fit residues: 35.9030 Evaluate side-chains 255 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 63 GLU Chi-restraints excluded: chain E residue 67 ARG 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 123 ILE 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 75 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 91 SER 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 99 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 102 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 HIS K 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.048549 restraints weight = 24584.662| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.45 r_work: 0.2580 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8358 Z= 0.184 Angle : 0.702 8.777 11334 Z= 0.363 Chirality : 0.047 0.188 1271 Planarity : 0.005 0.049 1433 Dihedral : 5.723 53.219 1267 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 6.24 % Allowed : 29.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.25), residues: 1022 helix: None (None), residues: 0 sheet: -0.25 (0.24), residues: 469 loop : -1.63 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 138 TYR 0.024 0.002 TYR H 33 PHE 0.024 0.002 PHE E 207 TRP 0.011 0.001 TRP A 38 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8342) covalent geometry : angle 0.68868 (11296) SS BOND : bond 0.00517 ( 10) SS BOND : angle 1.32530 ( 20) hydrogen bonds : bond 0.03816 ( 183) hydrogen bonds : angle 5.70728 ( 477) link_NAG-ASN : bond 0.00311 ( 6) link_NAG-ASN : angle 3.20632 ( 18) *********************** 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 274 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.8660 (t80) cc_final: 0.8453 (t80) REVERT: A 101 ASP cc_start: 0.7708 (t70) cc_final: 0.7449 (t0) REVERT: A 152 ASN cc_start: 0.8674 (t0) cc_final: 0.8365 (t0) REVERT: B 14 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.8538 (mtm) REVERT: B 130 ASP cc_start: 0.8618 (t0) cc_final: 0.8351 (t0) REVERT: B 203 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8969 (p) REVERT: H 63 LYS cc_start: 0.9290 (ptpp) cc_final: 0.9046 (mtmt) REVERT: I 74 THR cc_start: 0.8879 (p) cc_final: 0.8654 (p) REVERT: K 87 ASP cc_start: 0.8823 (t0) cc_final: 0.8506 (t0) outliers start: 55 outliers final: 46 residues processed: 255 average time/residue: 0.1007 time to fit residues: 33.2613 Evaluate side-chains 261 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 179 VAL 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 63 GLU Chi-restraints excluded: chain E residue 67 ARG 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 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 80 TYR Chi-restraints excluded: chain H residue 91 SER 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 72 SER 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 19 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 94 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.049208 restraints weight = 24799.511| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.44 r_work: 0.2590 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8358 Z= 0.157 Angle : 0.695 8.388 11334 Z= 0.357 Chirality : 0.046 0.227 1271 Planarity : 0.004 0.047 1433 Dihedral : 5.622 51.948 1267 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.78 % Allowed : 30.61 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.19 (0.24), residues: 474 loop : -1.60 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 13 TYR 0.022 0.002 TYR H 33 PHE 0.023 0.002 PHE E 207 TRP 0.012 0.001 TRP A 38 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8342) covalent geometry : angle 0.68497 (11296) SS BOND : bond 0.00513 ( 10) SS BOND : angle 1.13759 ( 20) hydrogen bonds : bond 0.03500 ( 183) hydrogen bonds : angle 5.60950 ( 477) link_NAG-ASN : bond 0.00334 ( 6) link_NAG-ASN : angle 2.94225 ( 18) *********************** 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 270 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 99 PHE cc_start: 0.8651 (t80) cc_final: 0.8323 (t80) REVERT: A 101 ASP cc_start: 0.7732 (t70) cc_final: 0.7495 (t0) REVERT: B 14 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8523 (mtm) REVERT: B 130 ASP cc_start: 0.8657 (t0) cc_final: 0.8395 (t0) REVERT: B 203 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8939 (p) REVERT: H 63 LYS cc_start: 0.9249 (ptpp) cc_final: 0.9022 (mtmt) REVERT: I 74 THR cc_start: 0.8950 (p) cc_final: 0.8719 (p) REVERT: K 87 ASP cc_start: 0.8852 (t0) cc_final: 0.8549 (t0) outliers start: 51 outliers final: 42 residues processed: 252 average time/residue: 0.1049 time to fit residues: 34.7644 Evaluate side-chains 255 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 179 VAL 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 55 GLU Chi-restraints excluded: chain E residue 67 ARG 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 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 91 SER Chi-restraints excluded: chain H residue 111 THR 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 72 SER Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 19 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 ASN ** 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 = 0.2947 r_free = 0.2947 target = 0.058930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.048258 restraints weight = 24758.804| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.45 r_work: 0.2564 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4222 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= 0.192 Angle : 0.744 8.799 11334 Z= 0.382 Chirality : 0.047 0.235 1271 Planarity : 0.005 0.039 1433 Dihedral : 5.827 50.310 1267 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.67 % Allowed : 30.84 % Favored : 63.49 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.16 (0.24), residues: 475 loop : -1.70 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 13 TYR 0.026 0.002 TYR H 33 PHE 0.022 0.002 PHE E 207 TRP 0.017 0.001 TRP A 38 HIS 0.004 0.002 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8342) covalent geometry : angle 0.73191 (11296) SS BOND : bond 0.00592 ( 10) SS BOND : angle 1.27457 ( 20) hydrogen bonds : bond 0.03821 ( 183) hydrogen bonds : angle 5.80793 ( 477) link_NAG-ASN : bond 0.00309 ( 6) link_NAG-ASN : angle 3.25390 ( 18) *********************** 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 267 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8963 (mm) cc_final: 0.8621 (mm) REVERT: B 14 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8541 (mtm) REVERT: B 130 ASP cc_start: 0.8701 (t0) cc_final: 0.8398 (t0) REVERT: B 203 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8932 (p) REVERT: E 162 LYS cc_start: 0.7672 (ttpp) cc_final: 0.7409 (ptmm) REVERT: H 63 LYS cc_start: 0.9230 (ptpp) cc_final: 0.9007 (mtmt) REVERT: I 74 THR cc_start: 0.9037 (p) cc_final: 0.8826 (p) REVERT: K 87 ASP cc_start: 0.8865 (t0) cc_final: 0.8570 (t0) outliers start: 50 outliers final: 43 residues processed: 248 average time/residue: 0.1041 time to fit residues: 33.7382 Evaluate side-chains 254 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 179 VAL Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 76 THR 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 67 ARG 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 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 91 SER 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 47 GLN Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 19 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 46 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.048921 restraints weight = 24819.337| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.45 r_work: 0.2578 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8358 Z= 0.174 Angle : 0.739 9.297 11334 Z= 0.378 Chirality : 0.047 0.224 1271 Planarity : 0.004 0.040 1433 Dihedral : 5.766 48.797 1267 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.56 % Allowed : 30.73 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.11 (0.24), residues: 475 loop : -1.68 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 13 TYR 0.037 0.002 TYR B 105 PHE 0.023 0.002 PHE E 207 TRP 0.018 0.001 TRP A 38 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8342) covalent geometry : angle 0.72875 (11296) SS BOND : bond 0.00539 ( 10) SS BOND : angle 1.15534 ( 20) hydrogen bonds : bond 0.03631 ( 183) hydrogen bonds : angle 5.69842 ( 477) link_NAG-ASN : bond 0.00344 ( 6) link_NAG-ASN : angle 3.07997 ( 18) *********************** 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 263 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 133 ILE cc_start: 0.8963 (mm) cc_final: 0.8658 (mm) REVERT: B 14 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8528 (mtm) REVERT: B 130 ASP cc_start: 0.8692 (t0) cc_final: 0.8389 (t0) REVERT: B 203 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8933 (p) REVERT: E 162 LYS cc_start: 0.7656 (ttpp) cc_final: 0.7448 (ptmm) REVERT: H 63 LYS cc_start: 0.9196 (ptpp) cc_final: 0.8963 (mtmt) REVERT: I 74 THR cc_start: 0.9009 (p) cc_final: 0.8804 (p) REVERT: K 87 ASP cc_start: 0.8875 (t0) cc_final: 0.8557 (t0) outliers start: 49 outliers final: 44 residues processed: 245 average time/residue: 0.1051 time to fit residues: 33.5396 Evaluate side-chains 255 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 179 VAL 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 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 67 ARG 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 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 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 21 ILE Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain J residue 19 LYS 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 85 SER 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 12 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.048161 restraints weight = 24809.047| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.46 r_work: 0.2557 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8358 Z= 0.203 Angle : 0.786 11.230 11334 Z= 0.402 Chirality : 0.048 0.256 1271 Planarity : 0.005 0.041 1433 Dihedral : 5.916 47.702 1267 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 5.44 % Allowed : 30.61 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.11 (0.24), residues: 474 loop : -1.70 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 77 TYR 0.037 0.002 TYR B 105 PHE 0.023 0.002 PHE E 207 TRP 0.016 0.002 TRP A 38 HIS 0.005 0.002 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 8342) covalent geometry : angle 0.77403 (11296) SS BOND : bond 0.00600 ( 10) SS BOND : angle 1.27021 ( 20) hydrogen bonds : bond 0.03908 ( 183) hydrogen bonds : angle 5.86193 ( 477) link_NAG-ASN : bond 0.00327 ( 6) link_NAG-ASN : angle 3.28123 ( 18) ********************** 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 261 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 213 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 133 ILE cc_start: 0.9001 (mm) cc_final: 0.8683 (mm) REVERT: A 153 ASN cc_start: 0.8264 (m-40) cc_final: 0.8026 (t0) REVERT: B 14 MET cc_start: 0.9323 (OUTLIER) cc_final: 0.8560 (mtm) REVERT: B 130 ASP cc_start: 0.8718 (t0) cc_final: 0.8398 (t0) REVERT: H 63 LYS cc_start: 0.9191 (ptpp) cc_final: 0.8975 (mtmt) REVERT: K 87 ASP cc_start: 0.8873 (t0) cc_final: 0.8572 (t0) outliers start: 48 outliers final: 42 residues processed: 246 average time/residue: 0.1032 time to fit residues: 33.1519 Evaluate side-chains 254 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 179 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain E residue 23 CYS Chi-restraints excluded: chain E residue 55 GLU 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 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 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 21 ILE Chi-restraints excluded: chain I residue 47 GLN Chi-restraints excluded: chain I residue 60 PHE Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 19 LYS 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 85 SER 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 57 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 45 optimal weight: 0.0170 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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** J 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.046755 restraints weight = 24830.874| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 2.45 r_work: 0.2526 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 8358 Z= 0.281 Angle : 0.858 10.986 11334 Z= 0.441 Chirality : 0.050 0.248 1271 Planarity : 0.005 0.044 1433 Dihedral : 6.200 41.752 1266 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.78 % Allowed : 31.07 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.26), residues: 1022 helix: None (None), residues: 0 sheet: -0.13 (0.24), residues: 473 loop : -1.80 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 77 TYR 0.038 0.003 TYR B 105 PHE 0.023 0.003 PHE E 207 TRP 0.017 0.002 TRP E 150 HIS 0.006 0.002 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 8342) covalent geometry : angle 0.84249 (11296) SS BOND : bond 0.00739 ( 10) SS BOND : angle 1.62433 ( 20) hydrogen bonds : bond 0.04530 ( 183) hydrogen bonds : angle 6.22635 ( 477) link_NAG-ASN : bond 0.00383 ( 6) link_NAG-ASN : angle 3.85365 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.40 seconds wall clock time: 39 minutes 11.70 seconds (2351.70 seconds total)