Starting phenix.real_space_refine on Sat Dec 28 06:28:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrh_60396/12_2024/8zrh_60396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrh_60396/12_2024/8zrh_60396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zrh_60396/12_2024/8zrh_60396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrh_60396/12_2024/8zrh_60396.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrh_60396/12_2024/8zrh_60396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrh_60396/12_2024/8zrh_60396.cif" } resolution = 3.6 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= 0.004 sd= 0.044 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 35 5.16 5 C 5151 2.51 5 N 1357 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8036 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1111 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "A" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1119 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 11, 'TRANS': 128} Chain: "D" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1045 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 10, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1119 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 11, 'TRANS': 128} Chain: "h" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "l" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 880 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 106} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "L" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 880 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 106} Time building chain proxies: 5.49, per 1000 atoms: 0.68 Number of scatterers: 8036 At special positions: 0 Unit cell: (110.622, 120.288, 123.51, 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 35 16.00 O 1493 8.00 N 1357 7.00 C 5151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.04 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 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: 1.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 44.6% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'B' and resid 12 through 18 removed outlier: 3.850A pdb=" N LEU B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 6.667A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.799A pdb=" N LEU B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU B 60 " --> pdb=" O ARG B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 110 removed outlier: 3.745A pdb=" N ARG B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 127 Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.783A pdb=" N PHE A 24 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 removed outlier: 3.846A pdb=" N LEU A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 75 removed outlier: 3.597A pdb=" N ARG A 56 " --> pdb=" O HIS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.786A pdb=" N ARG A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 4.312A pdb=" N ILE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.021A pdb=" N GLY A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 12 through 18 Processing helix chain 'D' and resid 19 through 24 removed outlier: 6.373A pdb=" N ASP D 22 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 removed outlier: 3.638A pdb=" N ASP D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.751A pdb=" N LEU D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 4.080A pdb=" N ARG D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 110 removed outlier: 3.736A pdb=" N CYS D 107 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 108 " --> pdb=" O HIS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.869A pdb=" N GLY D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 124 " --> pdb=" O VAL D 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 19 removed outlier: 4.008A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.672A pdb=" N LEU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 49 through 75 removed outlier: 3.767A pdb=" N LEU C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.610A pdb=" N LEU C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 111 removed outlier: 4.323A pdb=" N ILE C 97 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.504A pdb=" N VAL C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 87 through 91 removed outlier: 3.749A pdb=" N THR h 91 " --> pdb=" O ALA h 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 88 removed outlier: 4.144A pdb=" N VAL l 88 " --> pdb=" O ALA l 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.750A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.143A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'h' and resid 3 through 7 removed outlier: 4.121A pdb=" N GLN h 3 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER h 25 " --> pdb=" O GLN h 3 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU h 81 " --> pdb=" O LEU h 20 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS h 22 " --> pdb=" O LEU h 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'h' and resid 10 through 12 removed outlier: 7.099A pdb=" N MET h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TRP h 36 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR h 50 " --> pdb=" O ASP h 59 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP h 59 " --> pdb=" O TYR h 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'l' and resid 4 through 7 removed outlier: 3.574A pdb=" N PHE l 76 " --> pdb=" O CYS l 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR l 77 " --> pdb=" O SER l 70 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER l 70 " --> pdb=" O THR l 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'l' and resid 10 through 12 removed outlier: 3.695A pdb=" N LEU l 11 " --> pdb=" O LYS l 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU l 110 " --> pdb=" O LEU l 11 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET l 94 " --> pdb=" O SER l 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER l 39 " --> pdb=" O MET l 94 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N PHE l 38 " --> pdb=" O TYR l 54 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR l 54 " --> pdb=" O PHE l 38 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP l 40 " --> pdb=" O LEU l 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'l' and resid 10 through 12 removed outlier: 3.695A pdb=" N LEU l 11 " --> pdb=" O LYS l 108 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU l 110 " --> pdb=" O LEU l 11 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR l 102 " --> pdb=" O GLN l 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.120A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.100A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR H 50 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.574A pdb=" N PHE L 76 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER L 70 " --> pdb=" O THR L 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.696A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET L 94 " --> pdb=" O SER L 39 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER L 39 " --> pdb=" O MET L 94 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N PHE L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR L 54 " --> pdb=" O PHE L 38 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.696A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1068 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: 2.29 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1311 1.30 - 1.43: 2339 1.43 - 1.56: 4553 1.56 - 1.69: 3 1.69 - 1.82: 51 Bond restraints: 8257 Sorted by residual: bond pdb=" C LEU C 65 " pdb=" N MET C 66 " ideal model delta sigma weight residual 1.335 1.226 0.109 1.38e-02 5.25e+03 6.22e+01 bond pdb=" C GLY h 26 " pdb=" N PHE h 27 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.26e-02 6.30e+03 6.21e+01 bond pdb=" C GLY H 26 " pdb=" N PHE H 27 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.26e-02 6.30e+03 6.18e+01 bond pdb=" C LEU C 68 " pdb=" N ALA C 69 " ideal model delta sigma weight residual 1.335 1.437 -0.102 1.31e-02 5.83e+03 6.05e+01 bond pdb=" C SER A 106 " pdb=" N CYS A 107 " ideal model delta sigma weight residual 1.334 1.427 -0.093 1.23e-02 6.61e+03 5.70e+01 ... (remaining 8252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 10459 1.69 - 3.38: 628 3.38 - 5.07: 132 5.07 - 6.76: 26 6.76 - 8.44: 6 Bond angle restraints: 11251 Sorted by residual: angle pdb=" O LEU C 65 " pdb=" C LEU C 65 " pdb=" N MET C 66 " ideal model delta sigma weight residual 122.15 115.26 6.89 1.14e+00 7.69e-01 3.65e+01 angle pdb=" O ASN C 67 " pdb=" C ASN C 67 " pdb=" N LEU C 68 " ideal model delta sigma weight residual 122.12 115.90 6.22 1.06e+00 8.90e-01 3.44e+01 angle pdb=" N GLU A 8 " pdb=" CA GLU A 8 " pdb=" C GLU A 8 " ideal model delta sigma weight residual 113.50 106.34 7.16 1.23e+00 6.61e-01 3.39e+01 angle pdb=" O SER D 74 " pdb=" C SER D 74 " pdb=" N ASN D 75 " ideal model delta sigma weight residual 122.09 115.90 6.19 1.08e+00 8.57e-01 3.28e+01 angle pdb=" CA LEU C 65 " pdb=" C LEU C 65 " pdb=" N MET C 66 " ideal model delta sigma weight residual 117.39 124.29 -6.90 1.24e+00 6.50e-01 3.10e+01 ... (remaining 11246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4182 17.68 - 35.37: 513 35.37 - 53.05: 133 53.05 - 70.73: 18 70.73 - 88.42: 2 Dihedral angle restraints: 4848 sinusoidal: 1904 harmonic: 2944 Sorted by residual: dihedral pdb=" CA PRO D 5 " pdb=" C PRO D 5 " pdb=" N TYR D 6 " pdb=" CA TYR D 6 " ideal model delta harmonic sigma weight residual -180.00 -161.59 -18.41 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA GLN h 39 " pdb=" C GLN h 39 " pdb=" N VAL h 40 " pdb=" CA VAL h 40 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLN H 39 " pdb=" C GLN H 39 " pdb=" N VAL H 40 " pdb=" CA VAL H 40 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 854 0.041 - 0.083: 213 0.083 - 0.124: 123 0.124 - 0.165: 26 0.165 - 0.207: 14 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA GLN l 95 " pdb=" N GLN l 95 " pdb=" C GLN l 95 " pdb=" CB GLN l 95 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA GLN L 95 " pdb=" N GLN L 95 " pdb=" C GLN L 95 " pdb=" CB GLN L 95 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA LEU D 15 " pdb=" N LEU D 15 " pdb=" C LEU D 15 " pdb=" CB LEU D 15 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 1227 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 14 " -0.074 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO L 15 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 137 " 0.060 5.00e-02 4.00e+02 8.79e-02 1.24e+01 pdb=" N PRO A 138 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 56 " -0.250 9.50e-02 1.11e+02 1.12e-01 7.70e+00 pdb=" NE ARG C 56 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 56 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 56 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 56 " -0.008 2.00e-02 2.50e+03 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3325 2.89 - 3.39: 7856 3.39 - 3.89: 12376 3.89 - 4.40: 13430 4.40 - 4.90: 22346 Nonbonded interactions: 59333 Sorted by model distance: nonbonded pdb=" O ASN B 67 " pdb=" OG1 THR B 70 " model vdw 2.383 3.040 nonbonded pdb=" O ASP h 102 " pdb=" OG SER h 103 " model vdw 2.391 3.040 nonbonded pdb=" O ASP H 102 " pdb=" OG SER H 103 " model vdw 2.392 3.040 nonbonded pdb=" OG1 THR h 49 " pdb=" O ASP h 59 " model vdw 2.397 3.040 nonbonded pdb=" OG1 THR H 49 " pdb=" O ASP H 59 " model vdw 2.397 3.040 ... (remaining 59328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 40 or resid 50 through 141)) selection = (chain 'B' and (resid 3 through 40 or resid 50 through 141)) selection = (chain 'C' and (resid 3 through 40 or resid 50 through 141)) selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } 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 group one per residue 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: 0.370 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.760 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 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 : 0.007 0.109 8257 Z= 0.480 Angle : 0.928 8.445 11251 Z= 0.631 Chirality : 0.052 0.207 1230 Planarity : 0.008 0.112 1443 Dihedral : 16.052 88.418 2946 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.80 % Favored : 95.90 % Rotamer: Outliers : 1.82 % Allowed : 29.55 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.45 (0.27), residues: 1001 helix: 0.89 (0.27), residues: 346 sheet: 1.00 (0.42), residues: 162 loop : -0.30 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 102 HIS 0.005 0.001 HIS A 104 PHE 0.029 0.002 PHE B 110 TYR 0.017 0.002 TYR B 6 ARG 0.004 0.001 ARG l 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 292 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 LEU cc_start: 0.7070 (mt) cc_final: 0.6780 (mt) REVERT: B 57 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7922 (mm-40) REVERT: B 93 MET cc_start: 0.7641 (mtp) cc_final: 0.7216 (mtm) REVERT: B 127 ARG cc_start: 0.3549 (tpt170) cc_final: 0.3161 (tmt170) REVERT: A 30 LEU cc_start: 0.8373 (mp) cc_final: 0.8086 (mp) REVERT: A 107 CYS cc_start: 0.8189 (t) cc_final: 0.7437 (t) REVERT: A 108 LEU cc_start: 0.8185 (mt) cc_final: 0.7891 (mt) REVERT: D 59 ILE cc_start: 0.8184 (mm) cc_final: 0.7840 (mm) REVERT: D 107 CYS cc_start: 0.7752 (m) cc_final: 0.7085 (m) REVERT: C 118 TYR cc_start: 0.7504 (t80) cc_final: 0.7056 (t80) REVERT: h 7 SER cc_start: 0.6519 (m) cc_final: 0.6239 (t) REVERT: h 50 TYR cc_start: 0.5457 (p90) cc_final: 0.4753 (p90) REVERT: H 31 LYS cc_start: 0.7844 (mttt) cc_final: 0.7548 (mttt) REVERT: H 50 TYR cc_start: 0.7102 (p90) cc_final: 0.6734 (p90) REVERT: H 83 MET cc_start: 0.6271 (mtm) cc_final: 0.5911 (mtm) outliers start: 16 outliers final: 3 residues processed: 301 average time/residue: 0.1932 time to fit residues: 78.1521 Evaluate side-chains 275 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 272 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain h residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 90 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 104 HIS D 51 HIS ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8257 Z= 0.196 Angle : 0.667 8.527 11251 Z= 0.345 Chirality : 0.043 0.241 1230 Planarity : 0.006 0.059 1443 Dihedral : 4.765 52.302 1122 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 6.02 % Allowed : 23.30 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.76 (0.27), residues: 1001 helix: 1.42 (0.27), residues: 363 sheet: 0.30 (0.37), residues: 204 loop : -0.08 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 102 HIS 0.007 0.002 HIS D 51 PHE 0.018 0.002 PHE H 27 TYR 0.022 0.002 TYR A 88 ARG 0.004 0.001 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 296 time to evaluate : 0.957 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: B 57 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8029 (mm-40) REVERT: B 62 TRP cc_start: 0.7981 (t-100) cc_final: 0.7754 (t-100) REVERT: B 93 MET cc_start: 0.7860 (mtp) cc_final: 0.7374 (mtm) REVERT: B 112 ARG cc_start: 0.7329 (tpp-160) cc_final: 0.7120 (mmt-90) REVERT: A 107 CYS cc_start: 0.8279 (t) cc_final: 0.7687 (t) REVERT: C 53 THR cc_start: 0.8334 (p) cc_final: 0.8112 (p) REVERT: C 57 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: C 83 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5951 (mp0) REVERT: C 101 LEU cc_start: 0.8587 (mm) cc_final: 0.8380 (mm) REVERT: C 118 TYR cc_start: 0.7341 (t80) cc_final: 0.7130 (t80) REVERT: h 7 SER cc_start: 0.6816 (m) cc_final: 0.6465 (t) REVERT: h 19 ARG cc_start: 0.8206 (ptm160) cc_final: 0.7849 (ptp-170) REVERT: h 64 VAL cc_start: 0.7152 (m) cc_final: 0.6861 (p) REVERT: h 83 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.5987 (mpp) REVERT: H 31 LYS cc_start: 0.7851 (mttt) cc_final: 0.7619 (mttt) REVERT: H 108 SER cc_start: 0.8056 (p) cc_final: 0.7829 (p) outliers start: 53 outliers final: 27 residues processed: 317 average time/residue: 0.1872 time to fit residues: 80.5432 Evaluate side-chains 300 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain h residue 83 MET Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS D 51 HIS ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8257 Z= 0.227 Angle : 0.662 10.978 11251 Z= 0.340 Chirality : 0.043 0.185 1230 Planarity : 0.005 0.056 1443 Dihedral : 4.569 50.352 1118 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 5.80 % Allowed : 25.34 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.75 (0.27), residues: 1001 helix: 1.55 (0.27), residues: 358 sheet: 0.31 (0.37), residues: 192 loop : -0.20 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 109 HIS 0.019 0.002 HIS D 51 PHE 0.020 0.002 PHE D 24 TYR 0.042 0.002 TYR A 88 ARG 0.005 0.001 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 281 time to evaluate : 0.944 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: B 57 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8086 (mm-40) REVERT: B 62 TRP cc_start: 0.8030 (t-100) cc_final: 0.7647 (t-100) REVERT: B 93 MET cc_start: 0.7929 (mtp) cc_final: 0.7361 (mtt) REVERT: B 112 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.7200 (tpp-160) REVERT: D 61 CYS cc_start: 0.8786 (t) cc_final: 0.8302 (m) REVERT: C 53 THR cc_start: 0.8468 (p) cc_final: 0.8136 (p) REVERT: C 57 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: C 83 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: C 101 LEU cc_start: 0.8625 (mm) cc_final: 0.8391 (mm) REVERT: h 7 SER cc_start: 0.6901 (m) cc_final: 0.6574 (t) REVERT: h 64 VAL cc_start: 0.7140 (m) cc_final: 0.6868 (p) REVERT: h 95 PHE cc_start: 0.6232 (m-80) cc_final: 0.6021 (m-80) REVERT: l 29 LEU cc_start: 0.8254 (mt) cc_final: 0.7716 (mt) REVERT: l 31 HIS cc_start: 0.6684 (t-90) cc_final: 0.6252 (t-90) REVERT: H 4 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7038 (pp) REVERT: H 31 LYS cc_start: 0.7971 (mttt) cc_final: 0.7760 (mttt) outliers start: 51 outliers final: 34 residues processed: 304 average time/residue: 0.1945 time to fit residues: 81.7653 Evaluate side-chains 313 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 84 ASN Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 HIS D 52 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8257 Z= 0.191 Angle : 0.642 10.236 11251 Z= 0.324 Chirality : 0.042 0.217 1230 Planarity : 0.005 0.058 1443 Dihedral : 4.504 48.552 1118 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 4.77 % Allowed : 28.98 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.67 (0.27), residues: 1001 helix: 1.45 (0.27), residues: 363 sheet: 0.33 (0.37), residues: 192 loop : -0.26 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.007 0.001 HIS D 51 PHE 0.024 0.002 PHE D 24 TYR 0.053 0.002 TYR A 88 ARG 0.003 0.000 ARG h 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 279 time to evaluate : 0.851 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: B 57 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8062 (mm-40) REVERT: B 62 TRP cc_start: 0.8013 (t-100) cc_final: 0.7590 (t-100) REVERT: B 93 MET cc_start: 0.7911 (mtp) cc_final: 0.7447 (mtm) REVERT: B 112 ARG cc_start: 0.7399 (tpp-160) cc_final: 0.7139 (tpp-160) REVERT: A 53 THR cc_start: 0.7571 (p) cc_final: 0.6903 (t) REVERT: A 57 GLN cc_start: 0.8244 (mm-40) cc_final: 0.8032 (mm110) REVERT: A 107 CYS cc_start: 0.7857 (t) cc_final: 0.7285 (t) REVERT: A 108 LEU cc_start: 0.8572 (pp) cc_final: 0.8304 (pp) REVERT: D 61 CYS cc_start: 0.8713 (t) cc_final: 0.8253 (m) REVERT: D 110 PHE cc_start: 0.7645 (m-10) cc_final: 0.7381 (m-10) REVERT: C 72 VAL cc_start: 0.8922 (t) cc_final: 0.8655 (p) REVERT: C 83 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: C 88 TYR cc_start: 0.8053 (t80) cc_final: 0.7822 (t80) REVERT: C 118 TYR cc_start: 0.7682 (t80) cc_final: 0.7264 (t80) REVERT: h 7 SER cc_start: 0.6837 (m) cc_final: 0.6484 (t) REVERT: h 64 VAL cc_start: 0.7109 (m) cc_final: 0.6854 (p) REVERT: h 95 PHE cc_start: 0.6251 (m-80) cc_final: 0.6018 (m-80) REVERT: l 31 HIS cc_start: 0.6669 (t-90) cc_final: 0.6234 (t-90) REVERT: l 38 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7096 (m-10) REVERT: H 50 TYR cc_start: 0.7347 (p90) cc_final: 0.7088 (p90) REVERT: L 84 GLU cc_start: 0.7239 (pm20) cc_final: 0.6148 (pm20) outliers start: 42 outliers final: 34 residues processed: 293 average time/residue: 0.1905 time to fit residues: 75.6186 Evaluate side-chains 307 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8257 Z= 0.231 Angle : 0.661 9.382 11251 Z= 0.336 Chirality : 0.044 0.194 1230 Planarity : 0.005 0.061 1443 Dihedral : 4.581 49.866 1118 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 6.25 % Allowed : 28.52 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.57 (0.27), residues: 1001 helix: 1.44 (0.27), residues: 364 sheet: 0.12 (0.37), residues: 194 loop : -0.32 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS C 104 PHE 0.022 0.002 PHE D 24 TYR 0.041 0.002 TYR A 88 ARG 0.003 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 0.948 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: B 14 GLU cc_start: 0.8410 (mp0) cc_final: 0.8070 (mp0) REVERT: B 57 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8125 (mm-40) REVERT: B 93 MET cc_start: 0.7952 (mtp) cc_final: 0.7472 (mtm) REVERT: B 112 ARG cc_start: 0.7470 (tpp-160) cc_final: 0.7201 (tpp-160) REVERT: A 8 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: A 53 THR cc_start: 0.7576 (p) cc_final: 0.6933 (t) REVERT: A 57 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8175 (mm110) REVERT: A 107 CYS cc_start: 0.8088 (t) cc_final: 0.7459 (t) REVERT: D 30 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8291 (tt) REVERT: D 61 CYS cc_start: 0.8739 (t) cc_final: 0.8130 (m) REVERT: D 105 ILE cc_start: 0.8610 (mm) cc_final: 0.8394 (tp) REVERT: C 64 GLU cc_start: 0.7239 (tt0) cc_final: 0.6956 (mt-10) REVERT: C 72 VAL cc_start: 0.9000 (t) cc_final: 0.8789 (p) REVERT: h 64 VAL cc_start: 0.7108 (m) cc_final: 0.6874 (p) REVERT: h 95 PHE cc_start: 0.6211 (m-80) cc_final: 0.5939 (m-80) REVERT: l 31 HIS cc_start: 0.6734 (t-90) cc_final: 0.6313 (t-90) REVERT: l 33 ASN cc_start: 0.8441 (t0) cc_final: 0.7986 (p0) REVERT: l 38 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: H 36 TRP cc_start: 0.6851 (m100) cc_final: 0.6612 (m100) REVERT: H 50 TYR cc_start: 0.7296 (p90) cc_final: 0.6926 (p90) REVERT: H 59 ASP cc_start: 0.7867 (t0) cc_final: 0.7631 (t0) REVERT: L 59 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7863 (mtp180) REVERT: L 84 GLU cc_start: 0.7119 (pm20) cc_final: 0.5977 (pm20) outliers start: 55 outliers final: 43 residues processed: 305 average time/residue: 0.1915 time to fit residues: 79.5942 Evaluate side-chains 322 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8257 Z= 0.170 Angle : 0.645 9.594 11251 Z= 0.325 Chirality : 0.043 0.202 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.486 50.809 1118 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 5.34 % Allowed : 29.55 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.43 (0.27), residues: 1001 helix: 1.32 (0.26), residues: 370 sheet: -0.05 (0.36), residues: 210 loop : -0.37 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 HIS 0.005 0.001 HIS h 35 PHE 0.021 0.002 PHE H 27 TYR 0.055 0.002 TYR A 88 ARG 0.005 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8366 (mp0) cc_final: 0.8045 (mp0) REVERT: B 57 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8063 (mm-40) REVERT: B 93 MET cc_start: 0.7850 (mtp) cc_final: 0.7328 (mtm) REVERT: B 99 GLN cc_start: 0.8488 (mt0) cc_final: 0.7917 (tt0) REVERT: B 112 ARG cc_start: 0.7426 (tpp-160) cc_final: 0.7139 (tpp-160) REVERT: A 8 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6980 (tp30) REVERT: A 9 PHE cc_start: 0.7501 (m-80) cc_final: 0.6857 (m-10) REVERT: A 23 PHE cc_start: 0.3751 (OUTLIER) cc_final: 0.2828 (m-80) REVERT: A 51 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6727 (m-70) REVERT: A 57 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8127 (mm-40) REVERT: A 107 CYS cc_start: 0.8072 (t) cc_final: 0.7234 (t) REVERT: A 127 ARG cc_start: 0.3354 (OUTLIER) cc_final: 0.1959 (tmt170) REVERT: D 30 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8177 (tt) REVERT: D 61 CYS cc_start: 0.8722 (t) cc_final: 0.8083 (m) REVERT: C 64 GLU cc_start: 0.7235 (tt0) cc_final: 0.6937 (mt-10) REVERT: C 72 VAL cc_start: 0.8950 (t) cc_final: 0.8736 (p) REVERT: h 36 TRP cc_start: 0.6919 (m100) cc_final: 0.6678 (m100) REVERT: h 64 VAL cc_start: 0.7105 (m) cc_final: 0.6866 (p) REVERT: l 31 HIS cc_start: 0.6784 (t-90) cc_final: 0.6338 (t-90) REVERT: l 38 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.7308 (m-10) REVERT: H 18 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7757 (mt) REVERT: H 50 TYR cc_start: 0.7245 (p90) cc_final: 0.6946 (p90) REVERT: H 59 ASP cc_start: 0.7856 (t0) cc_final: 0.7619 (t0) REVERT: L 59 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7867 (mtp180) REVERT: L 84 GLU cc_start: 0.7282 (pm20) cc_final: 0.6116 (pm20) outliers start: 47 outliers final: 31 residues processed: 303 average time/residue: 0.1898 time to fit residues: 78.0158 Evaluate side-chains 307 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 0.0870 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8257 Z= 0.236 Angle : 0.685 9.764 11251 Z= 0.348 Chirality : 0.045 0.271 1230 Planarity : 0.005 0.061 1443 Dihedral : 4.679 53.241 1118 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.09 % Favored : 94.81 % Rotamer: Outliers : 5.11 % Allowed : 30.00 % Favored : 64.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.37 (0.27), residues: 1001 helix: 1.17 (0.27), residues: 371 sheet: 0.11 (0.37), residues: 194 loop : -0.40 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 47 HIS 0.006 0.001 HIS C 104 PHE 0.020 0.002 PHE D 24 TYR 0.054 0.002 TYR A 88 ARG 0.011 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 276 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8495 (mp0) cc_final: 0.8151 (mp0) REVERT: B 57 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8134 (mm-40) REVERT: B 62 TRP cc_start: 0.8171 (t-100) cc_final: 0.7921 (t-100) REVERT: B 93 MET cc_start: 0.7945 (mtp) cc_final: 0.7687 (mtp) REVERT: B 99 GLN cc_start: 0.8543 (mt0) cc_final: 0.7967 (tt0) REVERT: B 112 ARG cc_start: 0.7511 (tpp-160) cc_final: 0.6999 (tpp-160) REVERT: A 8 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: A 23 PHE cc_start: 0.3742 (OUTLIER) cc_final: 0.2772 (m-80) REVERT: A 51 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.7138 (m170) REVERT: A 57 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8297 (mm-40) REVERT: A 93 MET cc_start: 0.8105 (ttm) cc_final: 0.7763 (ttm) REVERT: A 105 ILE cc_start: 0.8910 (tp) cc_final: 0.8573 (tp) REVERT: A 127 ARG cc_start: 0.3474 (OUTLIER) cc_final: 0.2066 (tmt170) REVERT: D 30 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8302 (tt) REVERT: D 60 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8127 (mm) REVERT: D 61 CYS cc_start: 0.8673 (t) cc_final: 0.8110 (m) REVERT: D 101 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8414 (mp) REVERT: C 64 GLU cc_start: 0.7320 (tt0) cc_final: 0.6989 (mt-10) REVERT: h 64 VAL cc_start: 0.7077 (m) cc_final: 0.6856 (p) REVERT: l 31 HIS cc_start: 0.6911 (t-90) cc_final: 0.6472 (t-90) REVERT: l 33 ASN cc_start: 0.8565 (t0) cc_final: 0.8123 (p0) REVERT: l 38 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: l 72 SER cc_start: 0.7809 (p) cc_final: 0.7534 (m) REVERT: H 50 TYR cc_start: 0.7267 (p90) cc_final: 0.6996 (p90) REVERT: H 59 ASP cc_start: 0.7908 (t0) cc_final: 0.7670 (t0) REVERT: L 84 GLU cc_start: 0.7261 (pm20) cc_final: 0.6065 (pm20) outliers start: 45 outliers final: 32 residues processed: 295 average time/residue: 0.1851 time to fit residues: 74.3489 Evaluate side-chains 313 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.0470 chunk 89 optimal weight: 8.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8257 Z= 0.180 Angle : 0.661 9.652 11251 Z= 0.331 Chirality : 0.044 0.261 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.577 54.193 1118 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 4.77 % Allowed : 31.36 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.35 (0.27), residues: 1001 helix: 1.11 (0.27), residues: 372 sheet: 0.05 (0.37), residues: 194 loop : -0.36 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.005 0.001 HIS C 104 PHE 0.022 0.002 PHE A 9 TYR 0.052 0.002 TYR A 88 ARG 0.009 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8476 (mp0) cc_final: 0.8129 (mp0) REVERT: B 57 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8083 (mm-40) REVERT: B 62 TRP cc_start: 0.8164 (t-100) cc_final: 0.7912 (t-100) REVERT: B 93 MET cc_start: 0.7855 (mtp) cc_final: 0.7585 (mtp) REVERT: B 99 GLN cc_start: 0.8513 (mt0) cc_final: 0.7953 (tt0) REVERT: B 112 ARG cc_start: 0.7493 (tpp-160) cc_final: 0.7188 (mmt-90) REVERT: B 127 ARG cc_start: 0.3015 (tpt170) cc_final: 0.2583 (tmt170) REVERT: A 8 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7159 (tp30) REVERT: A 23 PHE cc_start: 0.3664 (OUTLIER) cc_final: 0.2749 (m-80) REVERT: A 57 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8184 (mm-40) REVERT: A 66 MET cc_start: 0.7176 (mmt) cc_final: 0.6896 (tpp) REVERT: A 93 MET cc_start: 0.8080 (ttm) cc_final: 0.7779 (ttm) REVERT: A 105 ILE cc_start: 0.8918 (tp) cc_final: 0.8590 (tp) REVERT: A 127 ARG cc_start: 0.3342 (OUTLIER) cc_final: 0.1864 (tmt170) REVERT: D 30 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8299 (tt) REVERT: D 60 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8081 (mm) REVERT: D 61 CYS cc_start: 0.8628 (t) cc_final: 0.8123 (m) REVERT: D 101 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8381 (mp) REVERT: C 64 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6985 (mt-10) REVERT: h 36 TRP cc_start: 0.6928 (m100) cc_final: 0.6676 (m100) REVERT: l 31 HIS cc_start: 0.6940 (t-90) cc_final: 0.6559 (t-90) REVERT: l 33 ASN cc_start: 0.8573 (t0) cc_final: 0.8117 (p0) REVERT: l 38 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7202 (m-10) REVERT: l 72 SER cc_start: 0.7967 (p) cc_final: 0.7737 (m) REVERT: l 94 MET cc_start: 0.3509 (ttm) cc_final: 0.3119 (mtm) REVERT: H 50 TYR cc_start: 0.7200 (p90) cc_final: 0.6971 (p90) REVERT: H 59 ASP cc_start: 0.7899 (t0) cc_final: 0.7650 (t0) REVERT: L 84 GLU cc_start: 0.7407 (pm20) cc_final: 0.7163 (pm20) outliers start: 42 outliers final: 29 residues processed: 296 average time/residue: 0.1857 time to fit residues: 74.5560 Evaluate side-chains 308 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8257 Z= 0.197 Angle : 0.693 11.704 11251 Z= 0.344 Chirality : 0.045 0.331 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.627 56.081 1118 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 4.43 % Allowed : 31.02 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.34 (0.27), residues: 1001 helix: 1.14 (0.27), residues: 372 sheet: 0.04 (0.37), residues: 194 loop : -0.39 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 47 HIS 0.006 0.001 HIS A 51 PHE 0.017 0.001 PHE A 9 TYR 0.056 0.002 TYR A 88 ARG 0.008 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8562 (mp0) cc_final: 0.8199 (mp0) REVERT: B 57 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8092 (mm-40) REVERT: B 62 TRP cc_start: 0.8162 (t-100) cc_final: 0.7931 (t-100) REVERT: B 93 MET cc_start: 0.7863 (mtp) cc_final: 0.7595 (mtp) REVERT: B 99 GLN cc_start: 0.8529 (mt0) cc_final: 0.7974 (tt0) REVERT: B 112 ARG cc_start: 0.7509 (tpp-160) cc_final: 0.6983 (tpp-160) REVERT: B 127 ARG cc_start: 0.3028 (tpt170) cc_final: 0.2603 (tmt170) REVERT: A 8 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7018 (tp30) REVERT: A 9 PHE cc_start: 0.7229 (m-80) cc_final: 0.6831 (m-10) REVERT: A 23 PHE cc_start: 0.3922 (OUTLIER) cc_final: 0.3070 (m-80) REVERT: A 53 THR cc_start: 0.7720 (p) cc_final: 0.7077 (t) REVERT: A 57 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8167 (mm-40) REVERT: A 93 MET cc_start: 0.8119 (ttm) cc_final: 0.7830 (ttm) REVERT: A 105 ILE cc_start: 0.8950 (tp) cc_final: 0.8599 (tp) REVERT: A 127 ARG cc_start: 0.3429 (OUTLIER) cc_final: 0.1954 (tmt170) REVERT: D 30 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8322 (tt) REVERT: D 60 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8132 (mm) REVERT: D 61 CYS cc_start: 0.8598 (t) cc_final: 0.8090 (m) REVERT: D 101 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8429 (mp) REVERT: D 102 TRP cc_start: 0.8712 (t60) cc_final: 0.8420 (t60) REVERT: C 18 PHE cc_start: 0.8743 (t80) cc_final: 0.8457 (t80) REVERT: C 64 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6993 (mt-10) REVERT: l 31 HIS cc_start: 0.6909 (t-90) cc_final: 0.6525 (t-90) REVERT: l 33 ASN cc_start: 0.8614 (t0) cc_final: 0.8216 (p0) REVERT: H 50 TYR cc_start: 0.7249 (p90) cc_final: 0.7015 (p90) REVERT: H 59 ASP cc_start: 0.7924 (t0) cc_final: 0.7664 (t0) REVERT: L 84 GLU cc_start: 0.7365 (pm20) cc_final: 0.7112 (pm20) outliers start: 39 outliers final: 31 residues processed: 301 average time/residue: 0.1866 time to fit residues: 76.5145 Evaluate side-chains 317 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 280 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 18 PHE Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.0370 chunk 24 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS h 57 ASN ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8257 Z= 0.319 Angle : 0.785 10.625 11251 Z= 0.411 Chirality : 0.050 0.269 1230 Planarity : 0.006 0.063 1443 Dihedral : 5.323 58.233 1118 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 4.20 % Allowed : 31.48 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.08 (0.27), residues: 1001 helix: 0.82 (0.26), residues: 371 sheet: -0.10 (0.37), residues: 184 loop : -0.70 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP H 47 HIS 0.006 0.002 HIS C 104 PHE 0.024 0.002 PHE A 9 TYR 0.049 0.002 TYR A 88 ARG 0.009 0.001 ARG A 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8573 (mp0) cc_final: 0.8006 (mp0) REVERT: B 57 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8296 (mm-40) REVERT: B 93 MET cc_start: 0.7919 (mtp) cc_final: 0.7665 (mtp) REVERT: B 112 ARG cc_start: 0.7725 (tpp-160) cc_final: 0.7340 (tpp-160) REVERT: B 127 ARG cc_start: 0.3277 (tpt170) cc_final: 0.2766 (tmt170) REVERT: A 8 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: A 23 PHE cc_start: 0.4088 (OUTLIER) cc_final: 0.3361 (m-80) REVERT: A 53 THR cc_start: 0.8141 (p) cc_final: 0.7483 (t) REVERT: A 57 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8359 (mm-40) REVERT: A 66 MET cc_start: 0.7286 (mmt) cc_final: 0.7029 (tpp) REVERT: A 105 ILE cc_start: 0.9053 (tp) cc_final: 0.8729 (tp) REVERT: D 30 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8410 (tt) REVERT: D 60 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8200 (mm) REVERT: D 61 CYS cc_start: 0.8655 (t) cc_final: 0.8156 (m) REVERT: D 101 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8370 (mp) REVERT: D 102 TRP cc_start: 0.8793 (t60) cc_final: 0.7713 (t60) REVERT: C 60 LEU cc_start: 0.8616 (mt) cc_final: 0.8219 (mt) REVERT: C 64 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7048 (mt-10) REVERT: h 13 GLN cc_start: 0.7495 (tm-30) cc_final: 0.6626 (tm-30) REVERT: h 48 LEU cc_start: 0.8475 (mt) cc_final: 0.8268 (mt) REVERT: l 31 HIS cc_start: 0.7038 (t-90) cc_final: 0.6761 (t-90) REVERT: l 33 ASN cc_start: 0.8645 (t0) cc_final: 0.8323 (p0) REVERT: H 50 TYR cc_start: 0.7256 (p90) cc_final: 0.7053 (p90) REVERT: H 52 TRP cc_start: 0.7740 (m-10) cc_final: 0.7005 (m-10) REVERT: H 59 ASP cc_start: 0.7990 (t0) cc_final: 0.7721 (t0) REVERT: H 83 MET cc_start: 0.6568 (mtm) cc_final: 0.6353 (mtt) REVERT: H 102 ASP cc_start: 0.8371 (t70) cc_final: 0.8058 (t0) REVERT: L 52 LEU cc_start: 0.7607 (mt) cc_final: 0.7362 (mt) outliers start: 37 outliers final: 29 residues processed: 314 average time/residue: 0.1803 time to fit residues: 77.5451 Evaluate side-chains 330 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN D 51 HIS h 57 ASN ** l 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.137073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.116926 restraints weight = 17664.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.120632 restraints weight = 10252.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123172 restraints weight = 6832.056| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8257 Z= 0.193 Angle : 0.748 14.416 11251 Z= 0.370 Chirality : 0.045 0.217 1230 Planarity : 0.005 0.059 1443 Dihedral : 4.871 59.407 1118 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 3.75 % Allowed : 32.27 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.14 (0.27), residues: 1001 helix: 1.05 (0.27), residues: 369 sheet: 0.02 (0.37), residues: 194 loop : -0.63 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP H 47 HIS 0.005 0.001 HIS h 35 PHE 0.020 0.002 PHE C 24 TYR 0.058 0.002 TYR A 88 ARG 0.008 0.001 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2099.25 seconds wall clock time: 38 minutes 35.00 seconds (2315.00 seconds total)