Starting phenix.real_space_refine on Thu May 1 07:37:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vrw_43488/05_2025/8vrw_43488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vrw_43488/05_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_43488/05_2025/8vrw_43488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vrw_43488/05_2025/8vrw_43488.map" model { file = "/net/cci-nas-00/data/ceres_data/8vrw_43488/05_2025/8vrw_43488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vrw_43488/05_2025/8vrw_43488.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: E, H, F, I, D, G Time building chain proxies: 6.20, per 1000 atoms: 0.60 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: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.78 Time building geometry restraints manager: 2.71 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.290 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (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 TRP 0.006 0.001 TRP B 61 HIS 0.006 0.001 HIS D 143 PHE 0.012 0.002 PHE H 17 TYR 0.004 0.001 TYR E 102 ARG 0.003 0.000 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.26053 ( 453) hydrogen bonds : angle 10.04489 ( 1233) SS BOND : bond 0.00142 ( 9) SS BOND : angle 0.61321 ( 18) covalent geometry : bond 0.00381 (10698) covalent geometry : angle 0.59745 (14547) *********************** 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 : 1.043 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: 0.2352 time to fit residues: 74.6229 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 : 1.449 ------------------------------------------------------------------------------- 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 103 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN E 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.199152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.171622 restraints weight = 14707.859| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 3.29 r_work: 0.4078 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 10707 Z= 0.325 Angle : 0.777 16.284 14565 Z= 0.404 Chirality : 0.050 0.175 1569 Planarity : 0.008 0.079 1899 Dihedral : 5.923 55.371 1395 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.39 % Allowed : 8.94 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.24), residues: 1254 helix: 0.96 (0.30), residues: 285 sheet: -1.10 (0.28), residues: 336 loop : -1.91 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 61 HIS 0.017 0.002 HIS A 143 PHE 0.038 0.003 PHE E 31 TYR 0.014 0.002 TYR B 32 ARG 0.005 0.001 ARG E 23 Details of bonding type rmsd hydrogen bonds : bond 0.05912 ( 453) hydrogen bonds : angle 7.70122 ( 1233) SS BOND : bond 0.00379 ( 9) SS BOND : angle 1.38637 ( 18) covalent geometry : bond 0.00725 (10698) covalent geometry : angle 0.77568 (14547) *********************** 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 218 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.7630 (OUTLIER) cc_final: 0.7350 (t) REVERT: B 155 PHE cc_start: 0.7878 (m-80) cc_final: 0.7661 (m-80) REVERT: C 115 MET cc_start: 0.4635 (mtp) cc_final: 0.4416 (mtp) REVERT: H 25 ARG cc_start: 0.5922 (ttt180) cc_final: 0.5553 (ttt180) outliers start: 39 outliers final: 18 residues processed: 200 average time/residue: 0.2268 time to fit residues: 70.2846 Evaluate side-chains 192 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP 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 38 VAL Chi-restraints excluded: chain B residue 100 THR 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 G residue 17 ASP 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 95 VAL Chi-restraints excluded: chain H residue 127 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN C 89 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.201735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.172611 restraints weight = 14741.857| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.38 r_work: 0.4106 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10707 Z= 0.197 Angle : 0.632 13.971 14565 Z= 0.324 Chirality : 0.045 0.137 1569 Planarity : 0.007 0.070 1899 Dihedral : 4.850 25.443 1388 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.78 % Allowed : 13.02 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.24), residues: 1254 helix: 1.28 (0.31), residues: 285 sheet: -0.93 (0.28), residues: 336 loop : -1.76 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 9 HIS 0.013 0.002 HIS D 143 PHE 0.022 0.002 PHE H 31 TYR 0.028 0.002 TYR H 32 ARG 0.003 0.000 ARG G 44 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 453) hydrogen bonds : angle 7.17141 ( 1233) SS BOND : bond 0.00207 ( 9) SS BOND : angle 0.78097 ( 18) covalent geometry : bond 0.00436 (10698) covalent geometry : angle 0.63212 (14547) *********************** 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 201 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 PHE cc_start: 0.7904 (m-80) cc_final: 0.7634 (m-80) REVERT: D 23 MET cc_start: 0.6605 (ptm) cc_final: 0.6395 (ppp) REVERT: D 101 GLU cc_start: 0.6694 (tp30) cc_final: 0.6440 (tp30) REVERT: G 101 GLU cc_start: 0.6862 (tt0) cc_final: 0.6597 (tt0) REVERT: H 25 ARG cc_start: 0.5825 (ttt180) cc_final: 0.5608 (ptm-80) REVERT: I 91 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6765 (mm-30) outliers start: 32 outliers final: 21 residues processed: 189 average time/residue: 0.1706 time to fit residues: 49.7848 Evaluate side-chains 185 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 119 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 144 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 175 VAL 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 38 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain I residue 81 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 47 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** 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 70 GLN I 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.196928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.173496 restraints weight = 14991.683| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.82 r_work: 0.4109 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10707 Z= 0.196 Angle : 0.630 15.001 14565 Z= 0.320 Chirality : 0.045 0.143 1569 Planarity : 0.007 0.068 1899 Dihedral : 4.815 23.404 1387 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.69 % Allowed : 14.41 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1254 helix: 1.39 (0.32), residues: 279 sheet: -0.76 (0.27), residues: 354 loop : -1.67 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 9 HIS 0.011 0.002 HIS H 177 PHE 0.023 0.002 PHE B 31 TYR 0.018 0.002 TYR E 83 ARG 0.003 0.000 ARG E 23 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 453) hydrogen bonds : angle 7.01657 ( 1233) SS BOND : bond 0.00248 ( 9) SS BOND : angle 0.69462 ( 18) covalent geometry : bond 0.00437 (10698) covalent geometry : angle 0.62958 (14547) *********************** 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 202 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 ARG cc_start: 0.5603 (ttt180) cc_final: 0.5339 (ptm-80) REVERT: I 91 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6616 (mm-30) outliers start: 31 outliers final: 22 residues processed: 188 average time/residue: 0.1751 time to fit residues: 50.6637 Evaluate side-chains 192 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 97 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 95 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 95 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 175 VAL 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 144 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 96 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 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 = 0.4524 r_free = 0.4524 target = 0.198614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.170357 restraints weight = 14776.994| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.33 r_work: 0.4111 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4101 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 : 0.614 15.393 14565 Z= 0.310 Chirality : 0.044 0.132 1569 Planarity : 0.007 0.068 1899 Dihedral : 4.784 22.205 1387 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.30 % Allowed : 14.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1254 helix: 1.51 (0.32), residues: 279 sheet: -0.67 (0.27), residues: 354 loop : -1.52 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 9 HIS 0.010 0.002 HIS H 177 PHE 0.029 0.002 PHE H 31 TYR 0.013 0.001 TYR E 83 ARG 0.002 0.000 ARG H 93 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 453) hydrogen bonds : angle 6.90610 ( 1233) SS BOND : bond 0.00190 ( 9) SS BOND : angle 0.45339 ( 18) covalent geometry : bond 0.00412 (10698) covalent geometry : angle 0.61407 (14547) *********************** 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 206 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.5987 (mtp) cc_final: 0.5642 (ttm) REVERT: E 25 ARG cc_start: 0.5606 (ttt180) cc_final: 0.5298 (ptm-80) REVERT: I 107 MET cc_start: 0.6042 (mtp) cc_final: 0.5583 (mtp) outliers start: 38 outliers final: 26 residues processed: 190 average time/residue: 0.2086 time to fit residues: 61.6729 Evaluate side-chains 189 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 VAL 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 95 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 92 LEU 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 91 VAL Chi-restraints excluded: chain E residue 95 VAL 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 94 ASN Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.196114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.169385 restraints weight = 14751.560| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 3.30 r_work: 0.4076 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.4306 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= 0.186 Angle : 0.615 15.657 14565 Z= 0.310 Chirality : 0.044 0.175 1569 Planarity : 0.007 0.068 1899 Dihedral : 4.732 17.384 1386 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.12 % Allowed : 15.45 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1254 helix: 1.40 (0.32), residues: 279 sheet: -0.60 (0.27), residues: 354 loop : -1.45 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 9 HIS 0.011 0.001 HIS D 143 PHE 0.021 0.002 PHE H 122 TYR 0.012 0.001 TYR E 83 ARG 0.003 0.000 ARG E 93 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 453) hydrogen bonds : angle 6.95496 ( 1233) SS BOND : bond 0.00228 ( 9) SS BOND : angle 0.39423 ( 18) covalent geometry : bond 0.00416 (10698) covalent geometry : angle 0.61553 (14547) *********************** 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 205 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.6857 (ptm) cc_final: 0.6488 (ttp) REVERT: A 101 GLU cc_start: 0.6703 (tt0) cc_final: 0.6429 (tt0) REVERT: E 25 ARG cc_start: 0.5643 (ttt180) cc_final: 0.5283 (ptm-80) REVERT: G 23 MET cc_start: 0.6607 (ptm) cc_final: 0.6230 (ttp) REVERT: H 12 LYS cc_start: 0.6399 (OUTLIER) cc_final: 0.6141 (mttt) REVERT: I 107 MET cc_start: 0.6056 (mtp) cc_final: 0.5664 (mtp) outliers start: 36 outliers final: 26 residues processed: 192 average time/residue: 0.1735 time to fit residues: 51.5803 Evaluate side-chains 193 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 VAL Chi-restraints excluded: chain A residue 106 ILE 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 95 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 106 ILE 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 91 VAL Chi-restraints excluded: chain E residue 95 VAL 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 160 VAL Chi-restraints excluded: chain H residue 12 LYS Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 75 optimal weight: 0.0770 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 83 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 HIS ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.198935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.171347 restraints weight = 14820.357| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 3.27 r_work: 0.4111 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.4431 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= 0.152 Angle : 0.584 14.341 14565 Z= 0.294 Chirality : 0.043 0.140 1569 Planarity : 0.006 0.067 1899 Dihedral : 4.597 17.135 1386 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.26 % Allowed : 16.49 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1254 helix: 1.31 (0.32), residues: 285 sheet: -0.53 (0.27), residues: 366 loop : -1.48 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 9 HIS 0.010 0.001 HIS D 149 PHE 0.022 0.002 PHE H 122 TYR 0.010 0.001 TYR E 83 ARG 0.002 0.000 ARG H 93 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 453) hydrogen bonds : angle 6.80068 ( 1233) SS BOND : bond 0.00158 ( 9) SS BOND : angle 0.32726 ( 18) covalent geometry : bond 0.00339 (10698) covalent geometry : angle 0.58451 (14547) *********************** 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 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.6768 (ptm) cc_final: 0.6429 (ttp) REVERT: A 101 GLU cc_start: 0.6559 (tt0) cc_final: 0.6305 (tt0) REVERT: E 25 ARG cc_start: 0.5557 (ttt180) cc_final: 0.5292 (ptm160) REVERT: G 23 MET cc_start: 0.6572 (ptm) cc_final: 0.6222 (ttp) REVERT: I 107 MET cc_start: 0.6059 (mtp) cc_final: 0.5706 (mtp) outliers start: 26 outliers final: 20 residues processed: 184 average time/residue: 0.1682 time to fit residues: 47.9080 Evaluate side-chains 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET 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 38 VAL Chi-restraints excluded: chain D residue 17 ASP 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 21 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.198600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.172383 restraints weight = 14633.976| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.22 r_work: 0.4089 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10707 Z= 0.164 Angle : 0.602 14.454 14565 Z= 0.301 Chirality : 0.043 0.174 1569 Planarity : 0.006 0.067 1899 Dihedral : 4.600 17.174 1386 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.69 % Allowed : 16.41 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.24), residues: 1254 helix: 1.19 (0.32), residues: 285 sheet: -0.51 (0.27), residues: 366 loop : -1.48 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 9 HIS 0.009 0.001 HIS D 143 PHE 0.024 0.002 PHE H 122 TYR 0.010 0.001 TYR H 83 ARG 0.002 0.000 ARG H 93 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 453) hydrogen bonds : angle 6.79799 ( 1233) SS BOND : bond 0.00167 ( 9) SS BOND : angle 0.30683 ( 18) covalent geometry : bond 0.00368 (10698) covalent geometry : angle 0.60266 (14547) *********************** 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 195 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.6834 (ptm) cc_final: 0.6469 (ttp) REVERT: A 55 GLU cc_start: 0.7205 (tp30) cc_final: 0.6692 (mp0) REVERT: A 101 GLU cc_start: 0.6552 (tt0) cc_final: 0.6292 (tt0) REVERT: E 25 ARG cc_start: 0.5590 (ttt180) cc_final: 0.5324 (ptm160) REVERT: G 23 MET cc_start: 0.6613 (ptm) cc_final: 0.6267 (ttp) outliers start: 31 outliers final: 27 residues processed: 184 average time/residue: 0.1713 time to fit residues: 48.8539 Evaluate side-chains 191 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 106 ILE 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 80 THR Chi-restraints excluded: chain D residue 106 ILE 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 21 THR Chi-restraints excluded: chain E residue 95 VAL 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 147 LEU Chi-restraints excluded: chain H residue 175 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 93 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.203471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.176690 restraints weight = 14257.345| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 3.27 r_work: 0.4078 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.4721 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= 0.174 Angle : 0.612 14.542 14565 Z= 0.306 Chirality : 0.043 0.131 1569 Planarity : 0.006 0.067 1899 Dihedral : 4.665 16.944 1386 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.69 % Allowed : 16.58 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1254 helix: 1.20 (0.32), residues: 285 sheet: -0.45 (0.27), residues: 363 loop : -1.49 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 9 HIS 0.009 0.001 HIS D 143 PHE 0.025 0.002 PHE H 122 TYR 0.011 0.001 TYR H 83 ARG 0.003 0.000 ARG H 93 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 453) hydrogen bonds : angle 6.79961 ( 1233) SS BOND : bond 0.00176 ( 9) SS BOND : angle 0.23625 ( 18) covalent geometry : bond 0.00392 (10698) covalent geometry : angle 0.61191 (14547) *********************** 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 192 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.6852 (ptm) cc_final: 0.6550 (ttp) REVERT: A 55 GLU cc_start: 0.7218 (tp30) cc_final: 0.6718 (mp0) REVERT: E 25 ARG cc_start: 0.5613 (ttt180) cc_final: 0.5303 (ptm160) REVERT: G 23 MET cc_start: 0.6588 (ptm) cc_final: 0.6215 (ttp) outliers start: 31 outliers final: 27 residues processed: 181 average time/residue: 0.1721 time to fit residues: 49.2411 Evaluate side-chains 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 106 ILE 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 80 THR Chi-restraints excluded: chain D residue 106 ILE 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 21 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 86 GLN 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 147 LEU Chi-restraints excluded: chain H residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.202233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.174991 restraints weight = 14202.307| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.22 r_work: 0.4046 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.4888 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= 0.194 Angle : 0.632 14.983 14565 Z= 0.317 Chirality : 0.044 0.136 1569 Planarity : 0.007 0.067 1899 Dihedral : 4.745 16.897 1386 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.60 % Allowed : 16.75 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1254 helix: 0.71 (0.31), residues: 303 sheet: -0.47 (0.27), residues: 363 loop : -1.73 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 9 HIS 0.010 0.001 HIS D 143 PHE 0.026 0.002 PHE H 122 TYR 0.012 0.001 TYR H 83 ARG 0.003 0.000 ARG H 93 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 453) hydrogen bonds : angle 6.87989 ( 1233) SS BOND : bond 0.00221 ( 9) SS BOND : angle 0.24875 ( 18) covalent geometry : bond 0.00437 (10698) covalent geometry : angle 0.63201 (14547) ********************** 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 195 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.6891 (ptm) cc_final: 0.6552 (ttp) REVERT: A 55 GLU cc_start: 0.7224 (tp30) cc_final: 0.6716 (mp0) REVERT: C 115 MET cc_start: 0.4818 (OUTLIER) cc_final: 0.4430 (mtp) REVERT: D 55 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: E 25 ARG cc_start: 0.5612 (ttt180) cc_final: 0.5290 (ptm160) REVERT: G 23 MET cc_start: 0.6634 (ptm) cc_final: 0.6242 (ttp) outliers start: 30 outliers final: 28 residues processed: 183 average time/residue: 0.1912 time to fit residues: 54.8287 Evaluate side-chains 194 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 106 ILE 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 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 80 THR Chi-restraints excluded: chain D residue 106 ILE 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 21 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 86 GLN 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 147 LEU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain I residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 84 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 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 156 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.203734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.177026 restraints weight = 14175.015| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.20 r_work: 0.4078 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10707 Z= 0.169 Angle : 0.612 13.873 14565 Z= 0.307 Chirality : 0.044 0.147 1569 Planarity : 0.006 0.066 1899 Dihedral : 4.684 16.830 1386 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.86 % Allowed : 16.67 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1254 helix: 1.19 (0.32), residues: 285 sheet: -0.47 (0.27), residues: 363 loop : -1.48 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 9 HIS 0.012 0.001 HIS G 143 PHE 0.033 0.002 PHE H 18 TYR 0.012 0.001 TYR H 83 ARG 0.002 0.000 ARG H 93 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 453) hydrogen bonds : angle 6.79950 ( 1233) SS BOND : bond 0.00186 ( 9) SS BOND : angle 0.20186 ( 18) covalent geometry : bond 0.00379 (10698) covalent geometry : angle 0.61221 (14547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6640.02 seconds wall clock time: 116 minutes 38.23 seconds (6998.23 seconds total)