Starting phenix.real_space_refine on Wed Mar 4 19:44:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsy_63359/03_2026/9lsy_63359_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsy_63359/03_2026/9lsy_63359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lsy_63359/03_2026/9lsy_63359_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsy_63359/03_2026/9lsy_63359_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lsy_63359/03_2026/9lsy_63359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsy_63359/03_2026/9lsy_63359.map" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6813 atoms to isotropic. 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 42 5.16 5 C 6452 2.51 5 N 1719 2.21 5 O 1947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10160 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1592 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "G" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1808 Classifications: {'peptide': 222} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1588 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1825 Classifications: {'peptide': 224} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 102} Chain breaks: 1 Chain: "E" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 99} Chain breaks: 1 Chain: "H" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Time building chain proxies: 2.51, per 1000 atoms: 0.25 Number of scatterers: 10160 At special positions: 0 Unit cell: (107.8, 104.5, 196.9, 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 42 16.00 O 1947 8.00 N 1719 7.00 C 6452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 26 " - pdb=" SG CYS G 98 " distance=2.04 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 98 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 114 " distance=2.05 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 431.5 milliseconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2414 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 34 sheets defined 3.6% alpha, 48.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'G' and resid 142 through 149 removed outlier: 3.725A pdb=" N THR G 146 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 206 removed outlier: 3.860A pdb=" N SER G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU G 206 " --> pdb=" O GLU G 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 202 through 206' Processing helix chain 'G' and resid 219 through 223 removed outlier: 3.687A pdb=" N VAL G 223 " --> pdb=" O LYS G 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 149 removed outlier: 3.725A pdb=" N THR B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.860A pdb=" N SER B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 206 " --> pdb=" O GLU B 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 206' Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.686A pdb=" N VAL B 223 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.891A pdb=" N THR E 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.890A pdb=" N THR H 109 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'D' and resid 16 through 17 removed outlier: 6.921A pdb=" N MET D 16 " --> pdb=" O GLU D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 53 removed outlier: 3.687A pdb=" N GLU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 37 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 91 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 98 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS D 106 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 47 through 53 removed outlier: 3.687A pdb=" N GLU D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE D 37 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 91 " --> pdb=" O GLN D 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 129 through 134 removed outlier: 3.507A pdb=" N GLY D 181 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU D 144 " --> pdb=" O TYR D 175 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU D 180 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU D 162 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS D 182 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 151 through 155 removed outlier: 3.598A pdb=" N ARG D 151 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR D 190 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 13 through 17 removed outlier: 6.034A pdb=" N VAL G 14 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR G 124 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG G 16 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TRP G 101 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR G 35 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU G 51 " --> pdb=" O TRP G 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU G 40 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG G 49 " --> pdb=" O LEU G 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 13 through 17 removed outlier: 6.034A pdb=" N VAL G 14 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR G 124 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG G 16 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 21 through 25 Processing sheet with id=AB1, first strand: chain 'G' and resid 135 through 138 removed outlier: 6.203A pdb=" N TYR G 193 " --> pdb=" O LYS G 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 135 through 138 removed outlier: 6.203A pdb=" N TYR G 193 " --> pdb=" O LYS G 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 167 through 168 removed outlier: 3.850A pdb=" N HIS G 210 " --> pdb=" O PHE G 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AB5, first strand: chain 'A' and resid 16 through 17 removed outlier: 6.921A pdb=" N MET A 16 " --> pdb=" O GLU A 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 47 through 53 removed outlier: 3.687A pdb=" N GLU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP A 39 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 53 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 37 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 91 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 98 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 106 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 47 through 53 removed outlier: 3.687A pdb=" N GLU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP A 39 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 53 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 37 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 91 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 129 through 134 removed outlier: 3.507A pdb=" N GLY A 181 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 144 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR A 175 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU A 180 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N GLU A 162 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS A 182 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 151 through 155 removed outlier: 3.598A pdb=" N ARG A 151 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 190 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 13 through 17 removed outlier: 6.034A pdb=" N VAL B 14 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR B 124 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG B 16 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TRP B 101 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR B 35 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 40 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ARG B 49 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 13 through 17 removed outlier: 6.034A pdb=" N VAL B 14 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR B 124 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG B 16 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 21 through 25 Processing sheet with id=AC4, first strand: chain 'B' and resid 135 through 138 removed outlier: 6.202A pdb=" N TYR B 193 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 135 through 138 removed outlier: 6.202A pdb=" N TYR B 193 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.849A pdb=" N HIS B 210 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 24 through 25 Processing sheet with id=AC8, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.726A pdb=" N LEU C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR C 69 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 22 through 26 Processing sheet with id=AD1, first strand: chain 'E' and resid 30 through 31 removed outlier: 6.638A pdb=" N VAL E 53 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL E 69 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP E 55 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.554A pdb=" N THR E 118 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 30 through 33 removed outlier: 6.727A pdb=" N LEU F 53 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR F 69 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP F 55 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 39 through 44 Processing sheet with id=AD5, first strand: chain 'H' and resid 30 through 31 removed outlier: 6.638A pdb=" N VAL H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.554A pdb=" N THR H 118 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 37 through 42 398 hydrogen bonds defined for protein. 981 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: 1.43 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.21: 1 1.21 - 1.36: 3302 1.36 - 1.52: 4797 1.52 - 1.68: 2236 1.68 - 1.83: 60 Bond restraints: 10396 Sorted by residual: bond pdb=" C TYR C 70 " pdb=" O TYR C 70 " ideal model delta sigma weight residual 1.234 1.053 0.180 1.44e-02 4.82e+03 1.57e+02 bond pdb=" C TYR C 69 " pdb=" N TYR C 70 " ideal model delta sigma weight residual 1.333 1.237 0.096 1.39e-02 5.18e+03 4.77e+01 bond pdb=" C TYR C 70 " pdb=" N THR C 71 " ideal model delta sigma weight residual 1.331 1.275 0.056 1.35e-02 5.49e+03 1.74e+01 bond pdb=" CA TYR C 70 " pdb=" C TYR C 70 " ideal model delta sigma weight residual 1.525 1.490 0.036 1.40e-02 5.10e+03 6.45e+00 bond pdb=" CA TYR C 70 " pdb=" CB TYR C 70 " ideal model delta sigma weight residual 1.531 1.495 0.036 1.51e-02 4.39e+03 5.61e+00 ... (remaining 10391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 13860 2.89 - 5.78: 211 5.78 - 8.67: 21 8.67 - 11.55: 1 11.55 - 14.44: 1 Bond angle restraints: 14094 Sorted by residual: angle pdb=" C TYR C 70 " pdb=" CA TYR C 70 " pdb=" CB TYR C 70 " ideal model delta sigma weight residual 111.51 125.95 -14.44 1.58e+00 4.01e-01 8.36e+01 angle pdb=" CA TYR C 70 " pdb=" CB TYR C 70 " pdb=" CG TYR C 70 " ideal model delta sigma weight residual 113.90 123.76 -9.86 1.80e+00 3.09e-01 3.00e+01 angle pdb=" N THR C 71 " pdb=" CA THR C 71 " pdb=" CB THR C 71 " ideal model delta sigma weight residual 114.17 109.41 4.76 1.14e+00 7.69e-01 1.74e+01 angle pdb=" N TYR C 70 " pdb=" CA TYR C 70 " pdb=" CB TYR C 70 " ideal model delta sigma weight residual 112.30 106.00 6.30 1.52e+00 4.33e-01 1.72e+01 angle pdb=" C ASP D 196 " pdb=" N ASN D 197 " pdb=" CA ASN D 197 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 ... (remaining 14089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 5907 14.55 - 29.11: 261 29.11 - 43.66: 48 43.66 - 58.22: 8 58.22 - 72.77: 10 Dihedral angle restraints: 6234 sinusoidal: 2481 harmonic: 3753 Sorted by residual: dihedral pdb=" CA ILE F 49 " pdb=" C ILE F 49 " pdb=" N SER F 50 " pdb=" CA SER F 50 " ideal model delta harmonic sigma weight residual -180.00 -135.63 -44.37 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" CA ILE C 49 " pdb=" C ILE C 49 " pdb=" N SER C 50 " pdb=" CA SER C 50 " ideal model delta harmonic sigma weight residual -180.00 -135.65 -44.35 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" C TYR C 70 " pdb=" N TYR C 70 " pdb=" CA TYR C 70 " pdb=" CB TYR C 70 " ideal model delta harmonic sigma weight residual -122.60 -143.98 21.38 0 2.50e+00 1.60e-01 7.32e+01 ... (remaining 6231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1559 0.165 - 0.331: 11 0.331 - 0.496: 2 0.496 - 0.662: 0 0.662 - 0.827: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CA TYR C 70 " pdb=" N TYR C 70 " pdb=" C TYR C 70 " pdb=" CB TYR C 70 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB ILE D 167 " pdb=" CA ILE D 167 " pdb=" CG1 ILE D 167 " pdb=" CG2 ILE D 167 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE A 167 " pdb=" CA ILE A 167 " pdb=" CG1 ILE A 167 " pdb=" CG2 ILE A 167 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 1570 not shown) Planarity restraints: 1771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 70 " -0.045 2.00e-02 2.50e+03 3.31e-02 2.19e+01 pdb=" CG TYR C 70 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 70 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR C 70 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR C 70 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 70 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 70 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR C 70 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 135 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO B 136 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 136 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 136 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 135 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO G 136 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 136 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 136 " -0.041 5.00e-02 4.00e+02 ... (remaining 1768 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2633 2.81 - 3.33: 7662 3.33 - 3.86: 15684 3.86 - 4.38: 16817 4.38 - 4.90: 31431 Nonbonded interactions: 74227 Sorted by model distance: nonbonded pdb=" OG1 THR H 118 " pdb=" OG SER H 121 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR E 118 " pdb=" OG SER E 121 " model vdw 2.289 3.040 nonbonded pdb=" OG SER A 156 " pdb=" OD1 ASP A 185 " model vdw 2.307 3.040 nonbonded pdb=" OG SER D 156 " pdb=" OD1 ASP D 185 " model vdw 2.308 3.040 nonbonded pdb=" O SER F 50 " pdb=" OH TYR F 91 " model vdw 2.340 3.040 ... (remaining 74222 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 5 through 147 or (resid 148 and (name N or name CA or name \ C or name O or name CB )) or resid 149 through 206)) } ncs_group { reference = (chain 'B' and resid 10 through 231) selection = chain 'G' } ncs_group { reference = (chain 'C' and resid 24 through 127) selection = chain 'F' } ncs_group { reference = (chain 'E' and resid 25 through 135) selection = chain 'H' } 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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.980 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 0.180 10406 Z= 0.308 Angle : 0.949 14.443 14114 Z= 0.549 Chirality : 0.060 0.827 1573 Planarity : 0.008 0.075 1771 Dihedral : 9.244 72.774 3790 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.35 % Allowed : 2.19 % Favored : 97.47 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.21), residues: 1267 helix: -5.30 (0.27), residues: 12 sheet: -0.63 (0.20), residues: 634 loop : -2.77 (0.20), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.060 0.004 TYR C 70 PHE 0.016 0.003 PHE A 145 TRP 0.021 0.002 TRP E 125 HIS 0.006 0.002 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00627 (10396) covalent geometry : angle 0.94756 (14094) SS BOND : bond 0.00924 ( 10) SS BOND : angle 1.72608 ( 20) hydrogen bonds : bond 0.19869 ( 340) hydrogen bonds : angle 9.87461 ( 981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8397 (mmm) cc_final: 0.8144 (mmm) REVERT: A 187 ASN cc_start: 0.7668 (p0) cc_final: 0.7271 (p0) REVERT: F 112 ASN cc_start: 0.6640 (t0) cc_final: 0.6362 (m-40) outliers start: 4 outliers final: 0 residues processed: 191 average time/residue: 0.1563 time to fit residues: 37.6486 Evaluate side-chains 92 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 122 GLN D 124 HIS D 195 HIS G 91 ASN G 182 GLN G 210 HIS A 124 HIS C 47 GLN C 110 GLN C 112 ASN ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN H 102 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.082021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.058613 restraints weight = 56885.589| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 6.66 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10406 Z= 0.136 Angle : 0.664 7.601 14114 Z= 0.356 Chirality : 0.046 0.160 1573 Planarity : 0.006 0.062 1771 Dihedral : 5.378 34.583 1387 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.22 % Allowed : 8.48 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.22), residues: 1267 helix: -3.78 (0.88), residues: 14 sheet: -0.13 (0.20), residues: 663 loop : -2.32 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 77 TYR 0.017 0.001 TYR B 154 PHE 0.008 0.001 PHE A 70 TRP 0.015 0.001 TRP G 79 HIS 0.005 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00300 (10396) covalent geometry : angle 0.66371 (14094) SS BOND : bond 0.00403 ( 10) SS BOND : angle 0.74762 ( 20) hydrogen bonds : bond 0.03992 ( 340) hydrogen bonds : angle 6.58604 ( 981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.9012 (tpp) cc_final: 0.8798 (tpp) REVERT: A 47 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 72 LYS cc_start: 0.9210 (pttt) cc_final: 0.8899 (ptpt) REVERT: B 194 MET cc_start: 0.8339 (pp-130) cc_final: 0.7746 (ppp) REVERT: C 59 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8840 (mppt) REVERT: C 110 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8350 (pp30) REVERT: E 111 MET cc_start: 0.8365 (tpt) cc_final: 0.8013 (tpt) REVERT: F 108 CYS cc_start: 0.7364 (p) cc_final: 0.6703 (m) REVERT: F 112 ASN cc_start: 0.4085 (t0) cc_final: 0.3880 (m110) REVERT: H 58 GLN cc_start: 0.7221 (tp40) cc_final: 0.6853 (mp10) outliers start: 14 outliers final: 6 residues processed: 111 average time/residue: 0.1204 time to fit residues: 17.9498 Evaluate side-chains 92 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain F residue 56 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN G 221 ASN A 60 ASN A 194 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.078781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.059189 restraints weight = 58402.014| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 5.14 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10406 Z= 0.222 Angle : 0.695 6.635 14114 Z= 0.371 Chirality : 0.046 0.162 1573 Planarity : 0.005 0.061 1771 Dihedral : 5.508 35.732 1387 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.75 % Allowed : 8.74 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.22), residues: 1267 helix: -3.57 (0.96), residues: 14 sheet: -0.21 (0.20), residues: 650 loop : -1.90 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 96 TYR 0.022 0.002 TYR G 52 PHE 0.038 0.002 PHE H 98 TRP 0.023 0.002 TRP G 198 HIS 0.016 0.002 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00504 (10396) covalent geometry : angle 0.69392 (14094) SS BOND : bond 0.00670 ( 10) SS BOND : angle 1.25521 ( 20) hydrogen bonds : bond 0.04430 ( 340) hydrogen bonds : angle 6.18254 ( 981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 47 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 72 LYS cc_start: 0.9269 (pttt) cc_final: 0.8857 (ptpt) REVERT: A 144 GLU cc_start: 0.8208 (pm20) cc_final: 0.8006 (pp20) REVERT: B 24 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 194 MET cc_start: 0.8392 (pp-130) cc_final: 0.7862 (ppp) REVERT: C 59 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8926 (mppt) REVERT: E 111 MET cc_start: 0.8676 (tpt) cc_final: 0.8197 (tpt) REVERT: F 108 CYS cc_start: 0.6473 (p) cc_final: 0.5973 (m) REVERT: F 112 ASN cc_start: 0.7291 (t0) cc_final: 0.6256 (m-40) REVERT: H 58 GLN cc_start: 0.7140 (tp40) cc_final: 0.6887 (tp40) outliers start: 20 outliers final: 10 residues processed: 98 average time/residue: 0.1049 time to fit residues: 14.4236 Evaluate side-chains 85 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 169 HIS Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 0.0000 chunk 123 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** 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 = 0.3982 r_free = 0.3982 target = 0.081193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.062731 restraints weight = 58212.046| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 5.24 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10406 Z= 0.139 Angle : 0.599 6.583 14114 Z= 0.320 Chirality : 0.044 0.162 1573 Planarity : 0.005 0.050 1771 Dihedral : 4.933 31.990 1387 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.31 % Allowed : 9.53 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.22), residues: 1267 helix: -3.05 (1.14), residues: 14 sheet: -0.00 (0.20), residues: 639 loop : -1.65 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 151 TYR 0.015 0.001 TYR G 52 PHE 0.026 0.001 PHE H 98 TRP 0.016 0.001 TRP A 33 HIS 0.005 0.001 HIS G 210 Details of bonding type rmsd covalent geometry : bond 0.00317 (10396) covalent geometry : angle 0.59833 (14094) SS BOND : bond 0.00502 ( 10) SS BOND : angle 0.90480 ( 20) hydrogen bonds : bond 0.03585 ( 340) hydrogen bonds : angle 5.63699 ( 981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8095 (mm-30) REVERT: D 164 ASP cc_start: 0.8066 (t0) cc_final: 0.7848 (t0) REVERT: A 47 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7623 (tm-30) REVERT: A 72 LYS cc_start: 0.9350 (pttt) cc_final: 0.8947 (ptpt) REVERT: A 144 GLU cc_start: 0.8267 (pm20) cc_final: 0.7924 (pp20) REVERT: A 168 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8905 (m) REVERT: B 24 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8698 (mp) REVERT: B 194 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7975 (ppp) REVERT: B 211 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7937 (ptt180) REVERT: C 59 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8923 (mppt) REVERT: E 20 GLN cc_start: 0.8175 (pp30) cc_final: 0.7662 (mm-40) REVERT: F 74 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6820 (tp) REVERT: F 112 ASN cc_start: 0.7670 (t0) cc_final: 0.6685 (m-40) REVERT: H 96 ARG cc_start: 0.8241 (tpp-160) cc_final: 0.7871 (tpp-160) REVERT: H 111 MET cc_start: 0.6419 (tpp) cc_final: 0.5547 (tpp) outliers start: 15 outliers final: 4 residues processed: 93 average time/residue: 0.0986 time to fit residues: 13.1840 Evaluate side-chains 85 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain F residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 67 optimal weight: 0.0170 chunk 106 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** 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 = 0.3929 r_free = 0.3929 target = 0.078172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056409 restraints weight = 57084.225| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 6.12 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10406 Z= 0.194 Angle : 0.637 7.846 14114 Z= 0.337 Chirality : 0.045 0.162 1573 Planarity : 0.005 0.050 1771 Dihedral : 5.068 34.506 1387 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.92 % Allowed : 9.88 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.23), residues: 1267 helix: -2.90 (1.18), residues: 14 sheet: -0.00 (0.20), residues: 642 loop : -1.60 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 96 TYR 0.019 0.002 TYR C 52 PHE 0.021 0.002 PHE H 98 TRP 0.016 0.001 TRP G 198 HIS 0.006 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00447 (10396) covalent geometry : angle 0.63630 (14094) SS BOND : bond 0.00648 ( 10) SS BOND : angle 1.18429 ( 20) hydrogen bonds : bond 0.03983 ( 340) hydrogen bonds : angle 5.71190 ( 981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7739 (mp) REVERT: G 194 MET cc_start: 0.8809 (ptp) cc_final: 0.8511 (ptt) REVERT: A 47 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 72 LYS cc_start: 0.9364 (pttt) cc_final: 0.9080 (ptpp) REVERT: A 144 GLU cc_start: 0.8363 (pm20) cc_final: 0.7978 (pp20) REVERT: B 24 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8665 (mp) REVERT: B 194 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8053 (ppp) REVERT: B 211 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7998 (ptt180) REVERT: C 59 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.8947 (mppt) REVERT: E 111 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8438 (tpt) REVERT: F 112 ASN cc_start: 0.6674 (t0) cc_final: 0.6051 (m-40) outliers start: 22 outliers final: 6 residues processed: 97 average time/residue: 0.1169 time to fit residues: 15.7377 Evaluate side-chains 86 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain F residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN F 57 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.078725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.054348 restraints weight = 57727.323| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 5.85 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10406 Z= 0.122 Angle : 0.586 8.498 14114 Z= 0.309 Chirality : 0.044 0.139 1573 Planarity : 0.004 0.050 1771 Dihedral : 4.705 31.475 1387 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.22 % Allowed : 11.19 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.23), residues: 1267 helix: -2.59 (1.28), residues: 14 sheet: 0.10 (0.21), residues: 641 loop : -1.41 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 215 TYR 0.013 0.001 TYR G 52 PHE 0.008 0.001 PHE A 70 TRP 0.017 0.001 TRP A 33 HIS 0.003 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00281 (10396) covalent geometry : angle 0.58586 (14094) SS BOND : bond 0.00454 ( 10) SS BOND : angle 0.92313 ( 20) hydrogen bonds : bond 0.03375 ( 340) hydrogen bonds : angle 5.38681 ( 981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.8954 (tpp) cc_final: 0.8650 (tpp) REVERT: G 24 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7862 (mp) REVERT: G 194 MET cc_start: 0.8819 (ptp) cc_final: 0.8543 (ptt) REVERT: A 16 MET cc_start: 0.8928 (tpp) cc_final: 0.8639 (tpp) REVERT: A 47 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 72 LYS cc_start: 0.9380 (pttt) cc_final: 0.8973 (ptpt) REVERT: A 144 GLU cc_start: 0.8339 (pm20) cc_final: 0.8049 (pp20) REVERT: B 24 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8697 (mp) REVERT: B 194 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8056 (ppp) REVERT: B 211 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8024 (ptt180) REVERT: C 59 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.8987 (mppt) REVERT: E 20 GLN cc_start: 0.7653 (pp30) cc_final: 0.7180 (mm-40) REVERT: E 111 MET cc_start: 0.8656 (tpt) cc_final: 0.8336 (tpt) REVERT: F 112 ASN cc_start: 0.5056 (t0) cc_final: 0.4848 (m-40) REVERT: H 101 MET cc_start: 0.7529 (tpp) cc_final: 0.7134 (tpp) outliers start: 14 outliers final: 6 residues processed: 88 average time/residue: 0.1120 time to fit residues: 13.6840 Evaluate side-chains 84 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain H residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.078706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.053491 restraints weight = 57248.857| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 5.87 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10406 Z= 0.118 Angle : 0.583 9.687 14114 Z= 0.307 Chirality : 0.044 0.154 1573 Planarity : 0.004 0.045 1771 Dihedral : 4.591 30.337 1387 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.75 % Allowed : 10.93 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.23), residues: 1267 helix: -2.36 (1.31), residues: 14 sheet: 0.07 (0.20), residues: 665 loop : -1.23 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 211 TYR 0.013 0.001 TYR G 52 PHE 0.038 0.001 PHE H 98 TRP 0.018 0.001 TRP A 33 HIS 0.003 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00272 (10396) covalent geometry : angle 0.58305 (14094) SS BOND : bond 0.00470 ( 10) SS BOND : angle 0.81175 ( 20) hydrogen bonds : bond 0.03309 ( 340) hydrogen bonds : angle 5.26758 ( 981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7897 (mp) REVERT: G 194 MET cc_start: 0.8740 (ptp) cc_final: 0.8470 (ptt) REVERT: A 47 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 72 LYS cc_start: 0.9343 (pttt) cc_final: 0.8987 (ptpt) REVERT: A 144 GLU cc_start: 0.8402 (pm20) cc_final: 0.8019 (pp20) REVERT: B 24 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 194 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.8069 (ppp) REVERT: B 211 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8009 (ptt180) REVERT: C 59 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9004 (mppt) REVERT: C 110 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8379 (pm20) REVERT: E 20 GLN cc_start: 0.8042 (pp30) cc_final: 0.7383 (mm-40) REVERT: F 112 ASN cc_start: 0.5116 (t0) cc_final: 0.4903 (m110) REVERT: H 101 MET cc_start: 0.7577 (tpp) cc_final: 0.7297 (tpp) outliers start: 20 outliers final: 9 residues processed: 89 average time/residue: 0.1122 time to fit residues: 13.9407 Evaluate side-chains 86 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain H residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 ASN ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.076617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.056870 restraints weight = 58458.529| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 5.12 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 10406 Z= 0.244 Angle : 0.697 11.390 14114 Z= 0.364 Chirality : 0.046 0.154 1573 Planarity : 0.005 0.066 1771 Dihedral : 5.182 35.437 1387 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.40 % Allowed : 11.54 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1267 helix: -2.48 (1.21), residues: 14 sheet: -0.01 (0.20), residues: 637 loop : -1.44 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 215 TYR 0.025 0.002 TYR C 52 PHE 0.041 0.002 PHE H 98 TRP 0.018 0.002 TRP A 33 HIS 0.007 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00560 (10396) covalent geometry : angle 0.69629 (14094) SS BOND : bond 0.00721 ( 10) SS BOND : angle 1.23660 ( 20) hydrogen bonds : bond 0.04245 ( 340) hydrogen bonds : angle 5.78327 ( 981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.8904 (tpp) cc_final: 0.8637 (tpt) REVERT: G 24 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 47 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 144 GLU cc_start: 0.8492 (pm20) cc_final: 0.7905 (pp20) REVERT: B 194 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8140 (ppp) REVERT: B 211 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8103 (ptt180) REVERT: C 59 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8997 (mppt) REVERT: C 110 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8332 (pm20) REVERT: F 112 ASN cc_start: 0.8081 (t0) cc_final: 0.7040 (m110) REVERT: H 96 ARG cc_start: 0.8252 (tpp-160) cc_final: 0.8035 (tpp-160) outliers start: 16 outliers final: 8 residues processed: 81 average time/residue: 0.0940 time to fit residues: 11.0059 Evaluate side-chains 80 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 210 HIS ** 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 = 0.3942 r_free = 0.3942 target = 0.078685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.056590 restraints weight = 57007.577| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 6.94 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10406 Z= 0.106 Angle : 0.609 12.408 14114 Z= 0.317 Chirality : 0.044 0.147 1573 Planarity : 0.004 0.058 1771 Dihedral : 4.562 29.884 1387 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.14 % Allowed : 12.50 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % 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 are not related in a simple way. whole: -0.79 (0.23), residues: 1267 helix: -2.05 (1.38), residues: 14 sheet: 0.16 (0.20), residues: 654 loop : -1.23 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 85 TYR 0.010 0.001 TYR G 52 PHE 0.028 0.001 PHE H 98 TRP 0.021 0.001 TRP A 33 HIS 0.002 0.000 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00238 (10396) covalent geometry : angle 0.60882 (14094) SS BOND : bond 0.00464 ( 10) SS BOND : angle 0.68594 ( 20) hydrogen bonds : bond 0.03137 ( 340) hydrogen bonds : angle 5.20730 ( 981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 144 GLU cc_start: 0.8445 (pm20) cc_final: 0.7961 (pp20) REVERT: B 187 MET cc_start: 0.8498 (tpp) cc_final: 0.8272 (ttm) REVERT: B 211 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7989 (ptt180) REVERT: C 59 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.8704 (mptt) REVERT: E 20 GLN cc_start: 0.8857 (pp30) cc_final: 0.8048 (mm-40) REVERT: F 112 ASN cc_start: 0.5875 (t0) cc_final: 0.5483 (m110) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.1052 time to fit residues: 12.0124 Evaluate side-chains 82 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain H residue 58 GLN Chi-restraints excluded: chain H residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 123 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 85 optimal weight: 0.0770 chunk 118 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 88 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.078374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.056321 restraints weight = 56251.709| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 6.73 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10406 Z= 0.118 Angle : 0.618 13.317 14114 Z= 0.318 Chirality : 0.044 0.152 1573 Planarity : 0.004 0.064 1771 Dihedral : 4.492 29.042 1387 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.05 % Allowed : 12.67 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % 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 are not related in a simple way. whole: -0.73 (0.23), residues: 1267 helix: -2.00 (1.38), residues: 14 sheet: 0.16 (0.20), residues: 666 loop : -1.18 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.013 0.001 TYR G 52 PHE 0.008 0.001 PHE B 139 TRP 0.022 0.001 TRP A 33 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00273 (10396) covalent geometry : angle 0.61828 (14094) SS BOND : bond 0.00486 ( 10) SS BOND : angle 0.74430 ( 20) hydrogen bonds : bond 0.03216 ( 340) hydrogen bonds : angle 5.11095 ( 981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7766 (mp) REVERT: A 47 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 144 GLU cc_start: 0.8458 (pm20) cc_final: 0.7953 (pp20) REVERT: C 59 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8941 (mppt) REVERT: E 20 GLN cc_start: 0.8817 (pp30) cc_final: 0.8080 (mm-40) REVERT: E 101 MET cc_start: 0.8366 (tpp) cc_final: 0.8120 (tpp) REVERT: F 112 ASN cc_start: 0.5963 (t0) cc_final: 0.5559 (m-40) outliers start: 12 outliers final: 7 residues processed: 80 average time/residue: 0.1087 time to fit residues: 12.3279 Evaluate side-chains 79 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 210 HIS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** H 58 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 = 0.3920 r_free = 0.3920 target = 0.077800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.053757 restraints weight = 57285.786| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.77 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10406 Z= 0.146 Angle : 0.631 13.202 14114 Z= 0.327 Chirality : 0.044 0.179 1573 Planarity : 0.004 0.045 1771 Dihedral : 4.604 30.216 1387 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.96 % Allowed : 12.94 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.23), residues: 1267 helix: -2.05 (1.35), residues: 14 sheet: 0.13 (0.20), residues: 665 loop : -1.20 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 211 TYR 0.015 0.001 TYR G 52 PHE 0.033 0.001 PHE H 98 TRP 0.013 0.001 TRP G 198 HIS 0.004 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00340 (10396) covalent geometry : angle 0.63027 (14094) SS BOND : bond 0.00561 ( 10) SS BOND : angle 0.84617 ( 20) hydrogen bonds : bond 0.03500 ( 340) hydrogen bonds : angle 5.21818 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.43 seconds wall clock time: 54 minutes 7.58 seconds (3247.58 seconds total)