Starting phenix.real_space_refine on Sat Aug 23 06:47:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vrw_43488/08_2025/8vrw_43488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vrw_43488/08_2025/8vrw_43488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vrw_43488/08_2025/8vrw_43488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vrw_43488/08_2025/8vrw_43488.map" model { file = "/net/cci-nas-00/data/ceres_data/8vrw_43488/08_2025/8vrw_43488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vrw_43488/08_2025/8vrw_43488.cif" } resolution = 3.03 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= 0.001 sd= 0.021 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 45 5.16 5 C 6663 2.51 5 N 1782 2.21 5 O 1923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10413 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1478 Classifications: {'peptide': 180} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 166} Chain: "B" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1548 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 177} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 445 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Restraints were copied for chains: D, G, E, H, F, I Time building chain proxies: 1.53, per 1000 atoms: 0.15 Number of scatterers: 10413 At special positions: 0 Unit cell: (101.868, 101.215, 106.439, 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 45 16.00 O 1923 8.00 N 1782 7.00 C 6663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 163 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 163 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 79 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 79 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 117 " - pdb=" SG CYS H 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 240.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 18 sheets defined 23.8% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 4.033A pdb=" N GLY A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 55 through 77 removed outlier: 3.931A pdb=" N ALA A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.868A pdb=" N GLN B 64 " --> pdb=" O TYR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.923A pdb=" N VAL B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASP B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 88 removed outlier: 4.472A pdb=" N SER B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 96 removed outlier: 3.600A pdb=" N GLN C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 removed outlier: 4.033A pdb=" N GLY D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG D 50 " --> pdb=" O GLU D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 50' Processing helix chain 'D' and resid 55 through 77 removed outlier: 3.931A pdb=" N ALA D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 64 removed outlier: 3.868A pdb=" N GLN E 64 " --> pdb=" O TYR E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.923A pdb=" N VAL E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 88 removed outlier: 4.472A pdb=" N SER E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 96 removed outlier: 3.600A pdb=" N GLN F 73 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 50 removed outlier: 4.033A pdb=" N GLY G 49 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 50' Processing helix chain 'G' and resid 55 through 77 removed outlier: 3.931A pdb=" N ALA G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 3.869A pdb=" N GLN H 64 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 78 removed outlier: 3.923A pdb=" N VAL H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 88 removed outlier: 4.473A pdb=" N SER H 88 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 96 removed outlier: 3.600A pdb=" N GLN I 73 " --> pdb=" O TYR I 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS I 80 " --> pdb=" O GLY I 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 15 removed outlier: 3.596A pdb=" N ARG B 13 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE A 24 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 40 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 3.599A pdb=" N ARG B 23 " --> pdb=" O PHE B 18 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 38 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR B 32 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLU B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 93 removed outlier: 6.225A pdb=" N PHE A 145 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 128 removed outlier: 4.504A pdb=" N TRP A 121 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 176 " --> pdb=" O CYS A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 104 removed outlier: 3.726A pdb=" N VAL B 159 " --> pdb=" O CYS B 117 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE B 155 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 143 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 136 through 138 removed outlier: 4.427A pdb=" N TRP B 131 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 130 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.597A pdb=" N ARG E 13 " --> pdb=" O GLN D 9 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE D 24 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 40 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.599A pdb=" N ARG E 23 " --> pdb=" O PHE E 18 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL E 38 " --> pdb=" O TYR E 30 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR E 32 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLU E 36 " --> pdb=" O TYR E 32 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 88 through 93 removed outlier: 6.225A pdb=" N PHE D 145 " --> pdb=" O LYS D 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 126 through 128 removed outlier: 4.504A pdb=" N TRP D 121 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS D 176 " --> pdb=" O CYS D 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 99 through 104 removed outlier: 3.726A pdb=" N VAL E 159 " --> pdb=" O CYS E 117 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE E 155 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 143 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 136 through 138 removed outlier: 4.428A pdb=" N TRP E 131 " --> pdb=" O GLU E 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG E 130 " --> pdb=" O GLN E 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 14 through 15 removed outlier: 3.597A pdb=" N ARG H 13 " --> pdb=" O GLN G 9 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE G 24 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU G 40 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 14 through 15 removed outlier: 3.599A pdb=" N ARG H 23 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL H 38 " --> pdb=" O TYR H 30 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR H 32 " --> pdb=" O GLU H 36 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLU H 36 " --> pdb=" O TYR H 32 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 88 through 93 removed outlier: 6.225A pdb=" N PHE G 145 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 126 through 128 removed outlier: 4.505A pdb=" N TRP G 121 " --> pdb=" O VAL G 128 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS G 176 " --> pdb=" O CYS G 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 99 through 104 removed outlier: 3.726A pdb=" N VAL H 159 " --> pdb=" O CYS H 117 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE H 155 " --> pdb=" O GLY H 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL H 143 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 136 through 138 removed outlier: 4.427A pdb=" N TRP H 131 " --> pdb=" O GLU H 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG H 130 " --> pdb=" O GLN H 174 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1233 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: 1.63 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2958 1.33 - 1.45: 1959 1.45 - 1.57: 5709 1.57 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 10698 Sorted by residual: bond pdb=" N VAL A 97 " pdb=" CA VAL A 97 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.46e+00 bond pdb=" N VAL D 97 " pdb=" CA VAL D 97 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.42e+00 bond pdb=" N VAL G 97 " pdb=" CA VAL G 97 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.36e+00 bond pdb=" N ASN A 103 " pdb=" CA ASN A 103 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.29e-02 6.01e+03 7.71e+00 bond pdb=" N ASN G 103 " pdb=" CA ASN G 103 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.29e-02 6.01e+03 7.60e+00 ... (remaining 10693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 13853 1.25 - 2.49: 537 2.49 - 3.74: 122 3.74 - 4.99: 29 4.99 - 6.23: 6 Bond angle restraints: 14547 Sorted by residual: angle pdb=" O SER G 95 " pdb=" C SER G 95 " pdb=" N PRO G 96 " ideal model delta sigma weight residual 121.71 117.93 3.78 6.40e-01 2.44e+00 3.48e+01 angle pdb=" O SER D 95 " pdb=" C SER D 95 " pdb=" N PRO D 96 " ideal model delta sigma weight residual 121.71 117.95 3.76 6.40e-01 2.44e+00 3.45e+01 angle pdb=" O SER A 95 " pdb=" C SER A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 121.71 117.99 3.72 6.40e-01 2.44e+00 3.38e+01 angle pdb=" CA SER G 95 " pdb=" C SER G 95 " pdb=" N PRO G 96 " ideal model delta sigma weight residual 117.71 121.61 -3.90 9.20e-01 1.18e+00 1.80e+01 angle pdb=" CA SER D 95 " pdb=" C SER D 95 " pdb=" N PRO D 96 " ideal model delta sigma weight residual 117.71 121.59 -3.88 9.20e-01 1.18e+00 1.77e+01 ... (remaining 14542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 5967 15.78 - 31.56: 354 31.56 - 47.34: 63 47.34 - 63.12: 12 63.12 - 78.89: 9 Dihedral angle restraints: 6405 sinusoidal: 2676 harmonic: 3729 Sorted by residual: dihedral pdb=" CD ARG G 50 " pdb=" NE ARG G 50 " pdb=" CZ ARG G 50 " pdb=" NH1 ARG G 50 " ideal model delta sinusoidal sigma weight residual 0.00 66.71 -66.71 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" CD ARG A 50 " pdb=" NE ARG A 50 " pdb=" CZ ARG A 50 " pdb=" NH1 ARG A 50 " ideal model delta sinusoidal sigma weight residual 0.00 66.69 -66.69 1 1.00e+01 1.00e-02 5.80e+01 dihedral pdb=" CD ARG D 50 " pdb=" NE ARG D 50 " pdb=" CZ ARG D 50 " pdb=" NH1 ARG D 50 " ideal model delta sinusoidal sigma weight residual 0.00 66.68 -66.68 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 6402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1282 0.052 - 0.105: 223 0.105 - 0.157: 52 0.157 - 0.209: 9 0.209 - 0.262: 3 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CA VAL D 132 " pdb=" N VAL D 132 " pdb=" C VAL D 132 " pdb=" CB VAL D 132 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA VAL A 132 " pdb=" N VAL A 132 " pdb=" C VAL A 132 " pdb=" CB VAL A 132 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL G 132 " pdb=" N VAL G 132 " pdb=" C VAL G 132 " pdb=" CB VAL G 132 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1566 not shown) Planarity restraints: 1899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 50 " -1.012 9.50e-02 1.11e+02 4.53e-01 1.24e+02 pdb=" NE ARG A 50 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A 50 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 50 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 50 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 50 " 1.012 9.50e-02 1.11e+02 4.53e-01 1.24e+02 pdb=" NE ARG G 50 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG G 50 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG G 50 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG G 50 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 50 " -1.011 9.50e-02 1.11e+02 4.53e-01 1.24e+02 pdb=" NE ARG D 50 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG D 50 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG D 50 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 50 " -0.024 2.00e-02 2.50e+03 ... (remaining 1896 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 117 2.64 - 3.20: 9236 3.20 - 3.77: 16113 3.77 - 4.33: 22483 4.33 - 4.90: 37126 Nonbonded interactions: 85075 Sorted by model distance: nonbonded pdb=" CD2 LEU C 88 " pdb=" CD2 LEU I 88 " model vdw 2.070 3.880 nonbonded pdb=" CD2 LEU C 88 " pdb=" CD2 LEU F 88 " model vdw 2.071 3.880 nonbonded pdb=" CD2 LEU F 88 " pdb=" CD2 LEU I 88 " model vdw 2.102 3.880 nonbonded pdb=" OE2 GLU H 36 " pdb=" CB ARG H 39 " model vdw 2.110 3.440 nonbonded pdb=" OE2 GLU E 36 " pdb=" CB ARG E 39 " model vdw 2.110 3.440 ... (remaining 85070 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 8.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.770 Find NCS groups from input model: 0.050 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10707 Z= 0.241 Angle : 0.597 6.233 14565 Z= 0.382 Chirality : 0.047 0.262 1569 Planarity : 0.023 0.453 1899 Dihedral : 10.401 78.894 3954 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.52 % Allowed : 5.21 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.34 (0.25), residues: 1254 helix: 1.15 (0.31), residues: 294 sheet: -1.23 (0.31), residues: 315 loop : -1.70 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.004 0.001 TYR E 102 PHE 0.012 0.002 PHE H 17 TRP 0.006 0.001 TRP B 61 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00381 (10698) covalent geometry : angle 0.59745 (14547) SS BOND : bond 0.00142 ( 9) SS BOND : angle 0.61321 ( 18) hydrogen bonds : bond 0.26053 ( 453) hydrogen bonds : angle 10.04489 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.334 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: E 18 PHE cc_start: 0.5973 (m-80) cc_final: 0.5572 (m-80) REVERT: G 30 GLU cc_start: 0.6842 (tt0) cc_final: 0.6642 (tt0) outliers start: 6 outliers final: 6 residues processed: 214 average time/residue: 0.0738 time to fit residues: 22.7943 Evaluate side-chains 199 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 193 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.204497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.175517 restraints weight = 15035.591| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.37 r_work: 0.4152 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10707 Z= 0.186 Angle : 0.627 10.426 14565 Z= 0.328 Chirality : 0.045 0.169 1569 Planarity : 0.007 0.070 1899 Dihedral : 5.525 56.870 1395 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.86 % Allowed : 7.81 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.12 (0.24), residues: 1254 helix: 1.66 (0.31), residues: 285 sheet: -0.92 (0.31), residues: 273 loop : -1.77 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 140 TYR 0.010 0.002 TYR B 32 PHE 0.029 0.002 PHE E 31 TRP 0.015 0.002 TRP B 61 HIS 0.014 0.002 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00402 (10698) covalent geometry : angle 0.62638 (14547) SS BOND : bond 0.00154 ( 9) SS BOND : angle 1.20761 ( 18) hydrogen bonds : bond 0.04479 ( 453) hydrogen bonds : angle 7.26079 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.6600 (mpp) cc_final: 0.6263 (mpp) REVERT: E 23 ARG cc_start: 0.6770 (ttp80) cc_final: 0.6250 (ttp-110) REVERT: F 94 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7635 (mtt180) REVERT: G 132 VAL cc_start: 0.7771 (t) cc_final: 0.7558 (m) REVERT: H 36 GLU cc_start: 0.6050 (tt0) cc_final: 0.5843 (tt0) REVERT: H 67 ILE cc_start: 0.5650 (OUTLIER) cc_final: 0.5370 (tp) REVERT: I 89 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6961 (mt0) outliers start: 33 outliers final: 16 residues processed: 194 average time/residue: 0.0781 time to fit residues: 22.2707 Evaluate side-chains 190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 89 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 0.0570 chunk 114 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 89 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** 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 = 0.4537 r_free = 0.4537 target = 0.198958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.169557 restraints weight = 14835.552| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 3.41 r_work: 0.4119 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10707 Z= 0.197 Angle : 0.624 13.899 14565 Z= 0.318 Chirality : 0.045 0.138 1569 Planarity : 0.007 0.065 1899 Dihedral : 4.690 27.002 1388 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.60 % Allowed : 11.72 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.99 (0.24), residues: 1254 helix: 1.51 (0.31), residues: 285 sheet: -0.78 (0.28), residues: 354 loop : -1.65 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 140 TYR 0.012 0.002 TYR E 83 PHE 0.025 0.002 PHE E 31 TRP 0.014 0.002 TRP E 9 HIS 0.012 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00441 (10698) covalent geometry : angle 0.62419 (14547) SS BOND : bond 0.00286 ( 9) SS BOND : angle 0.67681 ( 18) hydrogen bonds : bond 0.04252 ( 453) hydrogen bonds : angle 6.93417 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 ASN cc_start: 0.8059 (m-40) cc_final: 0.7779 (m110) REVERT: D 101 GLU cc_start: 0.6662 (tp30) cc_final: 0.6390 (tp30) REVERT: F 94 ARG cc_start: 0.7692 (mtt180) cc_final: 0.7343 (mtt180) REVERT: G 101 GLU cc_start: 0.6850 (tt0) cc_final: 0.6642 (tt0) REVERT: I 91 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6767 (mm-30) outliers start: 30 outliers final: 18 residues processed: 190 average time/residue: 0.0701 time to fit residues: 20.7981 Evaluate side-chains 183 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 52 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 77 optimal weight: 0.3980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 GLN I 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.203520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.175151 restraints weight = 14846.139| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 3.39 r_work: 0.4145 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10707 Z= 0.150 Angle : 0.570 12.094 14565 Z= 0.291 Chirality : 0.043 0.130 1569 Planarity : 0.006 0.065 1899 Dihedral : 4.514 22.498 1388 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.17 % Allowed : 13.80 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.74 (0.24), residues: 1254 helix: 1.75 (0.32), residues: 279 sheet: -0.62 (0.27), residues: 354 loop : -1.48 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 108 TYR 0.009 0.001 TYR E 83 PHE 0.018 0.002 PHE B 31 TRP 0.012 0.002 TRP B 9 HIS 0.010 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00332 (10698) covalent geometry : angle 0.57028 (14547) SS BOND : bond 0.00144 ( 9) SS BOND : angle 0.55251 ( 18) hydrogen bonds : bond 0.03606 ( 453) hydrogen bonds : angle 6.67543 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.6811 (ptm) cc_final: 0.6472 (ttp) REVERT: B 82 ASN cc_start: 0.8039 (m-40) cc_final: 0.7752 (m110) REVERT: B 155 PHE cc_start: 0.7899 (m-80) cc_final: 0.7619 (m-80) REVERT: E 142 MET cc_start: 0.2601 (mpt) cc_final: 0.2267 (mpt) REVERT: G 23 MET cc_start: 0.6552 (ptm) cc_final: 0.6106 (ttp) REVERT: I 91 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6744 (mm-30) outliers start: 25 outliers final: 20 residues processed: 180 average time/residue: 0.0795 time to fit residues: 21.6110 Evaluate side-chains 183 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain I residue 90 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN I 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.202700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.174252 restraints weight = 14684.142| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.33 r_work: 0.4114 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10707 Z= 0.184 Angle : 0.598 14.478 14565 Z= 0.304 Chirality : 0.044 0.146 1569 Planarity : 0.006 0.067 1899 Dihedral : 4.571 16.815 1386 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.69 % Allowed : 13.72 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.85 (0.24), residues: 1254 helix: 1.44 (0.31), residues: 285 sheet: -0.58 (0.27), residues: 354 loop : -1.54 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 108 TYR 0.015 0.002 TYR E 83 PHE 0.020 0.002 PHE B 31 TRP 0.014 0.002 TRP H 9 HIS 0.010 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00411 (10698) covalent geometry : angle 0.59856 (14547) SS BOND : bond 0.00226 ( 9) SS BOND : angle 0.50688 ( 18) hydrogen bonds : bond 0.03923 ( 453) hydrogen bonds : angle 6.75176 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 ASN cc_start: 0.8025 (m-40) cc_final: 0.7814 (m110) outliers start: 31 outliers final: 23 residues processed: 188 average time/residue: 0.0827 time to fit residues: 23.6263 Evaluate side-chains 191 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain I residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.197997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.173931 restraints weight = 15299.817| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.92 r_work: 0.4115 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10707 Z= 0.177 Angle : 0.588 14.217 14565 Z= 0.298 Chirality : 0.043 0.133 1569 Planarity : 0.006 0.067 1899 Dihedral : 4.575 16.848 1386 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.04 % Allowed : 14.50 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.76 (0.24), residues: 1254 helix: 1.48 (0.32), residues: 285 sheet: -0.57 (0.27), residues: 354 loop : -1.43 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 108 TYR 0.012 0.001 TYR E 83 PHE 0.021 0.002 PHE H 31 TRP 0.011 0.002 TRP H 9 HIS 0.009 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00396 (10698) covalent geometry : angle 0.58788 (14547) SS BOND : bond 0.00219 ( 9) SS BOND : angle 0.48820 ( 18) hydrogen bonds : bond 0.03811 ( 453) hydrogen bonds : angle 6.75058 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 27 residues processed: 188 average time/residue: 0.0806 time to fit residues: 23.3195 Evaluate side-chains 188 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain I residue 90 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.0000 chunk 77 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** 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 = 0.4527 r_free = 0.4527 target = 0.199089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.170806 restraints weight = 14927.182| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.34 r_work: 0.4112 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10707 Z= 0.162 Angle : 0.580 13.351 14565 Z= 0.296 Chirality : 0.044 0.178 1569 Planarity : 0.006 0.067 1899 Dihedral : 4.562 16.834 1386 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.86 % Allowed : 15.10 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.78 (0.24), residues: 1254 helix: 1.42 (0.31), residues: 285 sheet: -0.50 (0.27), residues: 366 loop : -1.49 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 108 TYR 0.010 0.001 TYR B 102 PHE 0.017 0.002 PHE H 18 TRP 0.011 0.001 TRP H 9 HIS 0.008 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00362 (10698) covalent geometry : angle 0.58042 (14547) SS BOND : bond 0.00200 ( 9) SS BOND : angle 0.37923 ( 18) hydrogen bonds : bond 0.03691 ( 453) hydrogen bonds : angle 6.71587 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.5930 (mtp) cc_final: 0.5584 (ttm) REVERT: C 115 MET cc_start: 0.4559 (OUTLIER) cc_final: 0.4244 (mtp) REVERT: G 23 MET cc_start: 0.6656 (ptm) cc_final: 0.6237 (ttp) REVERT: I 107 MET cc_start: 0.6093 (mtp) cc_final: 0.5651 (mtp) outliers start: 33 outliers final: 23 residues processed: 186 average time/residue: 0.0655 time to fit residues: 19.0385 Evaluate side-chains 186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain I residue 90 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 116 optimal weight: 0.0040 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 97 optimal weight: 0.3980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN I 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.199973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.171602 restraints weight = 15013.405| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 3.37 r_work: 0.4116 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10707 Z= 0.135 Angle : 0.574 11.983 14565 Z= 0.289 Chirality : 0.043 0.155 1569 Planarity : 0.006 0.066 1899 Dihedral : 4.494 16.199 1386 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.08 % Allowed : 16.41 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.65 (0.24), residues: 1254 helix: 1.46 (0.32), residues: 285 sheet: -0.37 (0.27), residues: 360 loop : -1.39 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 108 TYR 0.010 0.001 TYR H 83 PHE 0.023 0.002 PHE H 18 TRP 0.014 0.001 TRP E 9 HIS 0.007 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00302 (10698) covalent geometry : angle 0.57413 (14547) SS BOND : bond 0.00156 ( 9) SS BOND : angle 0.45942 ( 18) hydrogen bonds : bond 0.03543 ( 453) hydrogen bonds : angle 6.56267 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.6773 (ptm) cc_final: 0.6527 (ttp) REVERT: B 101 VAL cc_start: 0.7527 (m) cc_final: 0.7239 (m) REVERT: C 107 MET cc_start: 0.5879 (mtp) cc_final: 0.5538 (ttm) REVERT: C 115 MET cc_start: 0.4510 (OUTLIER) cc_final: 0.4213 (mtp) REVERT: E 142 MET cc_start: 0.2748 (mpt) cc_final: 0.2324 (mpt) REVERT: G 23 MET cc_start: 0.6677 (ptm) cc_final: 0.6308 (ttp) outliers start: 24 outliers final: 19 residues processed: 177 average time/residue: 0.0765 time to fit residues: 20.8036 Evaluate side-chains 182 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain I residue 90 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 94 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** 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 = 0.4519 r_free = 0.4519 target = 0.198131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.171017 restraints weight = 14786.287| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.36 r_work: 0.4072 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10707 Z= 0.169 Angle : 0.604 13.631 14565 Z= 0.304 Chirality : 0.044 0.155 1569 Planarity : 0.006 0.066 1899 Dihedral : 4.551 16.578 1386 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.91 % Allowed : 17.01 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -0.72 (0.24), residues: 1254 helix: 1.27 (0.32), residues: 285 sheet: -0.37 (0.27), residues: 360 loop : -1.40 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.012 0.001 TYR H 83 PHE 0.025 0.002 PHE H 18 TRP 0.019 0.002 TRP E 9 HIS 0.008 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00381 (10698) covalent geometry : angle 0.60437 (14547) SS BOND : bond 0.00195 ( 9) SS BOND : angle 0.35518 ( 18) hydrogen bonds : bond 0.03774 ( 453) hydrogen bonds : angle 6.65226 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.6831 (ptm) cc_final: 0.6540 (ttp) REVERT: C 107 MET cc_start: 0.6048 (mtp) cc_final: 0.5735 (ttm) REVERT: C 115 MET cc_start: 0.4478 (OUTLIER) cc_final: 0.4153 (mtp) REVERT: G 23 MET cc_start: 0.6649 (ptm) cc_final: 0.6248 (ttp) REVERT: I 107 MET cc_start: 0.6104 (mtp) cc_final: 0.5699 (mtp) outliers start: 22 outliers final: 19 residues processed: 171 average time/residue: 0.0714 time to fit residues: 19.0556 Evaluate side-chains 179 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain I residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN B 156 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.193211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.168446 restraints weight = 14819.235| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 3.13 r_work: 0.4044 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10707 Z= 0.279 Angle : 0.694 15.515 14565 Z= 0.355 Chirality : 0.047 0.166 1569 Planarity : 0.007 0.066 1899 Dihedral : 5.012 17.372 1386 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.08 % Allowed : 16.75 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.11 (0.24), residues: 1254 helix: 0.81 (0.32), residues: 285 sheet: -0.64 (0.28), residues: 354 loop : -1.54 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 93 TYR 0.016 0.002 TYR E 102 PHE 0.027 0.003 PHE H 18 TRP 0.026 0.003 TRP E 9 HIS 0.009 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00626 (10698) covalent geometry : angle 0.69388 (14547) SS BOND : bond 0.00452 ( 9) SS BOND : angle 0.47949 ( 18) hydrogen bonds : bond 0.04661 ( 453) hydrogen bonds : angle 7.13339 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 MET cc_start: 0.4597 (OUTLIER) cc_final: 0.4315 (mtp) outliers start: 24 outliers final: 18 residues processed: 176 average time/residue: 0.0686 time to fit residues: 19.1303 Evaluate side-chains 178 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain I residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.202247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.174869 restraints weight = 14114.051| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 3.26 r_work: 0.4061 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10707 Z= 0.200 Angle : 0.643 15.069 14565 Z= 0.326 Chirality : 0.045 0.184 1569 Planarity : 0.006 0.066 1899 Dihedral : 4.878 17.311 1386 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.74 % Allowed : 18.14 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.04 (0.24), residues: 1254 helix: 0.99 (0.32), residues: 279 sheet: -0.58 (0.27), residues: 366 loop : -1.55 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 93 TYR 0.012 0.001 TYR H 83 PHE 0.028 0.002 PHE H 18 TRP 0.021 0.002 TRP E 9 HIS 0.010 0.001 HIS G 143 Details of bonding type rmsd covalent geometry : bond 0.00449 (10698) covalent geometry : angle 0.64304 (14547) SS BOND : bond 0.00269 ( 9) SS BOND : angle 0.33003 ( 18) hydrogen bonds : bond 0.04065 ( 453) hydrogen bonds : angle 7.01741 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2832.35 seconds wall clock time: 49 minutes 12.62 seconds (2952.62 seconds total)