Starting phenix.real_space_refine on Sun Aug 4 11:13:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vrw_43488/08_2024/8vrw_43488.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vrw_43488/08_2024/8vrw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vrw_43488/08_2024/8vrw_43488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vrw_43488/08_2024/8vrw_43488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vrw_43488/08_2024/8vrw_43488.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vrw_43488/08_2024/8vrw_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 Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10413 Number of models: 1 Model: "" Number of chains: 9 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} Chain: "D" 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: "E" 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: "F" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 445 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Chain: "G" 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: "H" 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: "I" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 445 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Time building chain proxies: 6.37, per 1000 atoms: 0.61 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 E 15 " - pdb=" SG CYS E 79 " distance=2.03 Simple disulfide: pdb=" SG CYS E 117 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 163 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 79 " 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 - 3.50 Amino acid : False - 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: 3.67 Conformation dependent library (CDL) restraints added in 1.8 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: 1.25 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: 2.91 Time building geometry restraints manager: 4.04 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: 100.57 - 107.27: 503 107.27 - 113.96: 5812 113.96 - 120.66: 4231 120.66 - 127.36: 3865 127.36 - 134.06: 136 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: 0.00 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.600 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- 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 10698 Z= 0.247 Angle : 0.597 6.233 14547 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 208 time to evaluate : 1.127 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: 0.2055 time to fit residues: 63.4146 Evaluate side-chains 199 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 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 10698 Z= 0.469 Angle : 0.776 16.284 14547 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 *********************** 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 fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7598 (t) REVERT: C 115 MET cc_start: 0.4616 (mtp) cc_final: 0.4392 (mtp) outliers start: 39 outliers final: 18 residues processed: 200 average time/residue: 0.1780 time to fit residues: 54.0855 Evaluate side-chains 192 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10698 Z= 0.283 Angle : 0.633 13.876 14547 Z= 0.324 Chirality : 0.045 0.139 1569 Planarity : 0.007 0.069 1899 Dihedral : 4.859 25.910 1388 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.86 % Allowed : 13.02 % Favored : 84.11 % 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: -1.24 (0.24), residues: 1254 helix: 1.25 (0.31), residues: 285 sheet: -0.95 (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 0.023 0.002 PHE B 31 TYR 0.028 0.002 TYR H 32 ARG 0.003 0.000 ARG D 140 *********************** 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 200 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 25 ARG cc_start: 0.5456 (ttt180) cc_final: 0.4763 (ttt180) outliers start: 33 outliers final: 21 residues processed: 188 average time/residue: 0.1694 time to fit residues: 48.9371 Evaluate side-chains 183 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 110 optimal weight: 0.0980 chunk 84 optimal weight: 0.3980 chunk 58 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 H 149 GLN I 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10698 Z= 0.198 Angle : 0.572 11.823 14547 Z= 0.291 Chirality : 0.043 0.153 1569 Planarity : 0.006 0.065 1899 Dihedral : 4.618 23.486 1388 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.00 % Allowed : 15.19 % Favored : 82.81 % 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: 1.66 (0.32), residues: 279 sheet: -0.73 (0.27), residues: 354 loop : -1.57 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 9 HIS 0.011 0.002 HIS H 177 PHE 0.016 0.002 PHE B 31 TYR 0.013 0.001 TYR E 83 ARG 0.003 0.000 ARG D 140 *********************** 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 187 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 25 ARG cc_start: 0.5421 (ttt180) cc_final: 0.4795 (ttt180) REVERT: I 107 MET cc_start: 0.6153 (mtp) cc_final: 0.5873 (mtp) outliers start: 23 outliers final: 16 residues processed: 175 average time/residue: 0.1778 time to fit residues: 47.5667 Evaluate side-chains 179 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 31 ILE Chi-restraints excluded: chain G residue 94 ASN 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 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** F 87 ASN G 94 ASN H 70 GLN I 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10698 Z= 0.328 Angle : 0.645 15.594 14547 Z= 0.327 Chirality : 0.045 0.136 1569 Planarity : 0.007 0.068 1899 Dihedral : 4.822 22.566 1387 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.95 % Allowed : 14.76 % Favored : 82.29 % 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: -0.94 (0.24), residues: 1254 helix: 1.47 (0.32), residues: 279 sheet: -0.69 (0.27), residues: 354 loop : -1.58 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 9 HIS 0.011 0.002 HIS D 143 PHE 0.027 0.003 PHE H 122 TYR 0.015 0.002 TYR H 32 ARG 0.003 0.000 ARG H 93 *********************** 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 203 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 MET cc_start: 0.6219 (mtp) cc_final: 0.5952 (ttm) REVERT: H 12 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6715 (mttt) REVERT: H 25 ARG cc_start: 0.5448 (ttt180) cc_final: 0.4831 (ttt180) outliers start: 34 outliers final: 22 residues processed: 188 average time/residue: 0.1753 time to fit residues: 50.3048 Evaluate side-chains 188 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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 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 160 VAL Chi-restraints excluded: chain H residue 12 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10698 Z= 0.295 Angle : 0.631 14.364 14547 Z= 0.320 Chirality : 0.045 0.184 1569 Planarity : 0.007 0.068 1899 Dihedral : 4.776 17.735 1386 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.21 % Allowed : 15.36 % 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: -0.94 (0.24), residues: 1254 helix: 1.36 (0.32), residues: 279 sheet: -0.66 (0.27), residues: 354 loop : -1.54 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 9 HIS 0.010 0.002 HIS G 143 PHE 0.025 0.002 PHE B 122 TYR 0.013 0.001 TYR E 83 ARG 0.003 0.000 ARG E 93 *********************** 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 210 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7090 (ptm) cc_final: 0.6721 (ttp) REVERT: F 84 THR cc_start: 0.8133 (p) cc_final: 0.7791 (t) REVERT: G 23 MET cc_start: 0.6913 (ptm) cc_final: 0.6520 (ttp) REVERT: H 12 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6734 (mttt) outliers start: 37 outliers final: 25 residues processed: 194 average time/residue: 0.1697 time to fit residues: 50.9697 Evaluate side-chains 195 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 MET 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 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 12 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10698 Z= 0.274 Angle : 0.617 13.817 14547 Z= 0.313 Chirality : 0.044 0.150 1569 Planarity : 0.007 0.068 1899 Dihedral : 4.772 17.312 1386 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.21 % Allowed : 15.97 % Favored : 80.82 % 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: -1.10 (0.24), residues: 1254 helix: 0.97 (0.31), residues: 297 sheet: -0.65 (0.27), residues: 354 loop : -1.66 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 9 HIS 0.009 0.002 HIS G 143 PHE 0.025 0.002 PHE H 31 TYR 0.010 0.001 TYR H 32 ARG 0.003 0.000 ARG H 93 *********************** 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 208 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7093 (ptm) cc_final: 0.6736 (ttp) REVERT: B 101 VAL cc_start: 0.7653 (m) cc_final: 0.7365 (m) REVERT: C 107 MET cc_start: 0.6195 (mtp) cc_final: 0.5885 (ttm) REVERT: H 12 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6705 (mttt) REVERT: I 107 MET cc_start: 0.6284 (mtp) cc_final: 0.5908 (mtp) outliers start: 37 outliers final: 30 residues processed: 194 average time/residue: 0.1630 time to fit residues: 49.2961 Evaluate side-chains 199 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 73 MET 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 21 THR 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 F residue 115 MET Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 73 MET 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 12 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.0010 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 93 optimal weight: 0.0470 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 overall best weight: 0.4684 ------------------------------------------------------------------------------- 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** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10698 Z= 0.227 Angle : 0.594 12.615 14547 Z= 0.302 Chirality : 0.044 0.150 1569 Planarity : 0.006 0.068 1899 Dihedral : 4.650 18.551 1386 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.69 % Allowed : 17.19 % 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 (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: -0.82 (0.24), residues: 1254 helix: 1.40 (0.32), residues: 279 sheet: -0.62 (0.27), residues: 354 loop : -1.41 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 9 HIS 0.009 0.001 HIS D 149 PHE 0.030 0.002 PHE H 18 TYR 0.010 0.001 TYR H 83 ARG 0.002 0.000 ARG H 93 *********************** 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 198 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7095 (ptm) cc_final: 0.6753 (ttp) REVERT: A 55 GLU cc_start: 0.7233 (tp30) cc_final: 0.6717 (mp0) REVERT: C 107 MET cc_start: 0.6145 (mtp) cc_final: 0.5847 (ttm) REVERT: C 115 MET cc_start: 0.4709 (OUTLIER) cc_final: 0.4405 (mtp) REVERT: G 23 MET cc_start: 0.6802 (ptm) cc_final: 0.6421 (ttp) REVERT: I 107 MET cc_start: 0.6267 (mtp) cc_final: 0.5922 (mtp) outliers start: 31 outliers final: 25 residues processed: 185 average time/residue: 0.1642 time to fit residues: 47.5024 Evaluate side-chains 192 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 95 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 73 MET 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 175 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 73 MET 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 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 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN I 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 10698 Z= 0.561 Angle : 0.793 17.225 14547 Z= 0.410 Chirality : 0.051 0.189 1569 Planarity : 0.007 0.068 1899 Dihedral : 5.486 20.021 1386 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.21 % Allowed : 16.67 % 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 (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: -1.55 (0.23), residues: 1254 helix: 0.41 (0.31), residues: 279 sheet: -0.78 (0.28), residues: 348 loop : -1.85 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP H 9 HIS 0.013 0.002 HIS D 149 PHE 0.043 0.004 PHE H 31 TYR 0.017 0.003 TYR H 83 ARG 0.004 0.001 ARG D 76 *********************** 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 199 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7369 (tp30) cc_final: 0.6799 (mp0) REVERT: C 115 MET cc_start: 0.4845 (OUTLIER) cc_final: 0.4515 (mtp) outliers start: 37 outliers final: 27 residues processed: 185 average time/residue: 0.1712 time to fit residues: 48.4748 Evaluate side-chains 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 95 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 73 MET Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 HIS Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 21 THR 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 73 MET 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 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN B 149 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 HIS ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10698 Z= 0.239 Angle : 0.625 14.823 14547 Z= 0.316 Chirality : 0.044 0.185 1569 Planarity : 0.007 0.069 1899 Dihedral : 4.912 19.794 1386 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.52 % Allowed : 17.36 % 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 (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: -1.18 (0.24), residues: 1254 helix: 0.99 (0.32), residues: 279 sheet: -0.79 (0.27), residues: 375 loop : -1.62 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 9 HIS 0.008 0.001 HIS G 143 PHE 0.028 0.002 PHE H 122 TYR 0.011 0.001 TYR H 83 ARG 0.003 0.000 ARG B 39 ********************** 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 fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7241 (tp30) cc_final: 0.6738 (mp0) REVERT: B 101 VAL cc_start: 0.7392 (m) cc_final: 0.7096 (m) REVERT: C 115 MET cc_start: 0.4687 (OUTLIER) cc_final: 0.4341 (mtp) outliers start: 29 outliers final: 25 residues processed: 185 average time/residue: 0.1674 time to fit residues: 47.9831 Evaluate side-chains 188 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP 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 100 THR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 106 ILE 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 100 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 73 MET 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 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 29 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 97 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN B 149 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** G 143 HIS ** 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 = 0.4497 r_free = 0.4497 target = 0.194409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.167938 restraints weight = 14514.654| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.13 r_work: 0.4056 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10698 Z= 0.240 Angle : 0.623 15.039 14547 Z= 0.313 Chirality : 0.044 0.149 1569 Planarity : 0.007 0.069 1899 Dihedral : 4.820 18.408 1386 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.69 % Allowed : 17.80 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.00 (0.24), residues: 1254 helix: 1.16 (0.32), residues: 279 sheet: -0.71 (0.27), residues: 375 loop : -1.51 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 9 HIS 0.009 0.001 HIS D 149 PHE 0.030 0.002 PHE H 18 TYR 0.014 0.001 TYR H 83 ARG 0.003 0.000 ARG H 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2666.88 seconds wall clock time: 48 minutes 8.92 seconds (2888.92 seconds total)