Starting phenix.real_space_refine on Wed Jan 15 04:05:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrh_60396/01_2025/8zrh_60396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrh_60396/01_2025/8zrh_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_60396/01_2025/8zrh_60396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrh_60396/01_2025/8zrh_60396.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrh_60396/01_2025/8zrh_60396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrh_60396/01_2025/8zrh_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-5571/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: 5.15, per 1000 atoms: 0.64 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 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: 0.96 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: 2.16 Time building geometry restraints manager: 2.25 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: 0.490 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.220 Find NCS groups from input model: 0.310 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- 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: 0.1948 time to fit residues: 79.0006 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 : 0.866 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.151885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.132502 restraints weight = 17915.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.136352 restraints weight = 10261.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138884 restraints weight = 6650.706| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 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 : 0.935 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: 0.8195 (mm-40) cc_final: 0.7914 (mm-40) REVERT: B 62 TRP cc_start: 0.8103 (t-100) cc_final: 0.7889 (t-100) REVERT: B 93 MET cc_start: 0.7819 (mtp) cc_final: 0.7346 (mtm) REVERT: B 112 ARG cc_start: 0.7346 (tpp-160) cc_final: 0.7142 (mmt-90) REVERT: A 107 CYS cc_start: 0.8048 (t) cc_final: 0.7481 (t) REVERT: C 57 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: C 83 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: C 101 LEU cc_start: 0.8632 (mm) cc_final: 0.8431 (mm) REVERT: h 7 SER cc_start: 0.6721 (m) cc_final: 0.6388 (t) REVERT: h 19 ARG cc_start: 0.8218 (ptm160) cc_final: 0.7858 (ptp-170) REVERT: h 64 VAL cc_start: 0.7245 (m) cc_final: 0.6932 (p) REVERT: h 83 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.5875 (mpp) REVERT: H 31 LYS cc_start: 0.7872 (mttt) cc_final: 0.7633 (mttt) REVERT: H 108 SER cc_start: 0.8070 (p) cc_final: 0.7850 (p) outliers start: 53 outliers final: 27 residues processed: 317 average time/residue: 0.1888 time to fit residues: 81.0316 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 : 1.075 ------------------------------------------------------------------------------- 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 95 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 60 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 78 optimal weight: 0.0020 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.142924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.123005 restraints weight = 18028.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.126881 restraints weight = 10351.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.129513 restraints weight = 6748.453| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2972 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= 0.197 Angle : 0.645 10.920 11251 Z= 0.327 Chirality : 0.042 0.186 1230 Planarity : 0.005 0.056 1443 Dihedral : 4.497 49.750 1118 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 5.57 % Allowed : 25.11 % Favored : 69.32 % 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: 0.75 (0.27), residues: 1001 helix: 1.56 (0.27), residues: 363 sheet: 0.42 (0.37), residues: 182 loop : -0.28 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 109 HIS 0.014 0.002 HIS D 51 PHE 0.019 0.002 PHE D 24 TYR 0.040 0.002 TYR A 88 ARG 0.005 0.001 ARG L 66 *********************** 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 320 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7950 (mm-40) REVERT: B 62 TRP cc_start: 0.8099 (t-100) cc_final: 0.7661 (t-100) REVERT: B 93 MET cc_start: 0.7861 (mtp) cc_final: 0.7342 (mtt) REVERT: B 112 ARG cc_start: 0.7390 (tpp-160) cc_final: 0.7177 (tpp-160) REVERT: D 61 CYS cc_start: 0.8750 (t) cc_final: 0.8335 (m) REVERT: D 102 TRP cc_start: 0.8326 (t-100) cc_final: 0.8107 (t-100) REVERT: C 57 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: C 83 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6124 (mp0) REVERT: C 101 LEU cc_start: 0.8645 (mm) cc_final: 0.8421 (mm) REVERT: h 7 SER cc_start: 0.6770 (m) cc_final: 0.6451 (t) REVERT: h 13 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6908 (tm-30) REVERT: h 64 VAL cc_start: 0.7294 (m) cc_final: 0.7006 (p) REVERT: h 95 PHE cc_start: 0.6374 (m-80) cc_final: 0.6168 (m-80) REVERT: l 29 LEU cc_start: 0.8318 (mt) cc_final: 0.7751 (mt) REVERT: l 31 HIS cc_start: 0.6783 (t-90) cc_final: 0.6283 (t-90) REVERT: l 33 ASN cc_start: 0.8308 (t0) cc_final: 0.8032 (t0) REVERT: H 18 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7902 (mt) REVERT: H 31 LYS cc_start: 0.7939 (mttt) cc_final: 0.7734 (mttt) REVERT: H 36 TRP cc_start: 0.6891 (m100) cc_final: 0.6678 (m100) REVERT: L 84 GLU cc_start: 0.7287 (pm20) cc_final: 0.6369 (pm20) outliers start: 49 outliers final: 34 residues processed: 294 average time/residue: 0.1847 time to fit residues: 73.8229 Evaluate side-chains 311 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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 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 57 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 83 GLU 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 18 LEU 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 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 9 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 HIS H 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.143659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123613 restraints weight = 17880.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.127450 restraints weight = 10333.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.130077 restraints weight = 6823.678| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3479 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= 0.209 Angle : 0.657 12.818 11251 Z= 0.330 Chirality : 0.042 0.187 1230 Planarity : 0.005 0.059 1443 Dihedral : 4.558 50.059 1118 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 5.00 % Allowed : 27.73 % Favored : 67.27 % 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: 1.47 (0.27), residues: 363 sheet: 0.26 (0.37), residues: 192 loop : -0.23 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.007 0.001 HIS D 51 PHE 0.029 0.002 PHE D 24 TYR 0.053 0.002 TYR A 88 ARG 0.003 0.000 ARG C 56 *********************** 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 320 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 0.913 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 57 GLN cc_start: 0.8274 (mm-40) cc_final: 0.8004 (mm-40) REVERT: B 62 TRP cc_start: 0.8076 (t-100) cc_final: 0.7638 (t-100) REVERT: B 93 MET cc_start: 0.7847 (mtp) cc_final: 0.7422 (mtm) REVERT: B 112 ARG cc_start: 0.7428 (tpp-160) cc_final: 0.7190 (tpp-160) REVERT: A 53 THR cc_start: 0.7540 (p) cc_final: 0.7071 (t) REVERT: A 55 LEU cc_start: 0.8636 (tp) cc_final: 0.8288 (tt) REVERT: A 107 CYS cc_start: 0.7621 (t) cc_final: 0.7060 (t) REVERT: D 61 CYS cc_start: 0.8708 (t) cc_final: 0.8193 (m) REVERT: D 102 TRP cc_start: 0.8351 (t-100) cc_final: 0.8141 (t-100) REVERT: C 72 VAL cc_start: 0.8997 (t) cc_final: 0.8717 (p) REVERT: C 83 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: C 87 SER cc_start: 0.7445 (OUTLIER) cc_final: 0.7240 (p) REVERT: C 88 TYR cc_start: 0.8093 (t80) cc_final: 0.7851 (t80) REVERT: h 7 SER cc_start: 0.6802 (m) cc_final: 0.6461 (t) REVERT: h 13 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7118 (tm-30) REVERT: h 64 VAL cc_start: 0.7227 (m) cc_final: 0.6960 (p) REVERT: h 95 PHE cc_start: 0.6378 (m-80) cc_final: 0.6135 (m-80) REVERT: l 31 HIS cc_start: 0.6860 (t-90) cc_final: 0.6368 (t-90) REVERT: l 33 ASN cc_start: 0.8305 (t0) cc_final: 0.8074 (t0) REVERT: l 38 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7039 (m-10) REVERT: l 94 MET cc_start: 0.3512 (OUTLIER) cc_final: 0.2565 (mtm) REVERT: H 31 LYS cc_start: 0.7980 (mttt) cc_final: 0.7773 (mttt) REVERT: L 59 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7820 (mtp180) REVERT: L 84 GLU cc_start: 0.7205 (pm20) cc_final: 0.6126 (pm20) outliers start: 44 outliers final: 33 residues processed: 292 average time/residue: 0.1869 time to fit residues: 74.2087 Evaluate side-chains 307 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 114 THR 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 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 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 h residue 84 ASN 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 l residue 94 MET 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 99 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.140834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120645 restraints weight = 17579.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.124369 restraints weight = 10197.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.126819 restraints weight = 6779.635| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4148 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= 0.231 Angle : 0.670 9.985 11251 Z= 0.338 Chirality : 0.043 0.188 1230 Planarity : 0.005 0.061 1443 Dihedral : 4.686 52.670 1118 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 6.48 % Allowed : 27.05 % Favored : 66.48 % 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: 0.50 (0.27), residues: 1001 helix: 1.37 (0.27), residues: 364 sheet: 0.06 (0.37), residues: 194 loop : -0.33 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 47 HIS 0.007 0.001 HIS C 104 PHE 0.027 0.002 PHE D 24 TYR 0.048 0.002 TYR A 88 ARG 0.007 0.000 ARG C 56 *********************** 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 347 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 0.877 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 14 GLU cc_start: 0.8348 (mp0) cc_final: 0.8054 (mp0) REVERT: B 57 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8027 (mm-40) REVERT: B 93 MET cc_start: 0.7887 (mtp) cc_final: 0.7470 (mtm) REVERT: B 112 ARG cc_start: 0.7484 (tpp-160) cc_final: 0.7247 (tpp-160) REVERT: A 8 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: A 107 CYS cc_start: 0.7919 (t) cc_final: 0.7270 (t) REVERT: D 61 CYS cc_start: 0.8641 (t) cc_final: 0.8149 (m) REVERT: D 102 TRP cc_start: 0.8405 (t-100) cc_final: 0.8037 (t-100) REVERT: C 57 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: C 64 GLU cc_start: 0.7192 (tt0) cc_final: 0.6863 (mt-10) REVERT: C 72 VAL cc_start: 0.9092 (t) cc_final: 0.8869 (p) REVERT: C 87 SER cc_start: 0.7586 (OUTLIER) cc_final: 0.7277 (t) REVERT: C 118 TYR cc_start: 0.7604 (t80) cc_final: 0.7077 (t80) REVERT: h 13 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7085 (tm-30) REVERT: h 64 VAL cc_start: 0.7183 (m) cc_final: 0.6930 (p) REVERT: h 95 PHE cc_start: 0.6355 (m-80) cc_final: 0.6077 (m-80) REVERT: l 31 HIS cc_start: 0.6907 (t-90) cc_final: 0.6437 (t-90) REVERT: l 33 ASN cc_start: 0.8403 (t0) cc_final: 0.8173 (t0) REVERT: l 38 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: H 18 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7754 (mt) REVERT: H 31 LYS cc_start: 0.7994 (mttt) cc_final: 0.7781 (mttt) REVERT: H 36 TRP cc_start: 0.7021 (m100) cc_final: 0.6820 (m100) REVERT: H 59 ASP cc_start: 0.7925 (t0) cc_final: 0.7663 (t0) outliers start: 57 outliers final: 41 residues processed: 313 average time/residue: 0.1818 time to fit residues: 78.0118 Evaluate side-chains 324 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER 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 27 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 28 ARG 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 97 ILE 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 57 GLN 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 42 LEU 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 18 LEU Chi-restraints excluded: chain H residue 40 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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** h 57 ASN ** l 95 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.132139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.112251 restraints weight = 17721.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.115845 restraints weight = 10280.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.118264 restraints weight = 6837.522| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8257 Z= 0.410 Angle : 0.807 9.668 11251 Z= 0.429 Chirality : 0.050 0.212 1230 Planarity : 0.006 0.063 1443 Dihedral : 5.611 58.960 1118 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 7.73 % Allowed : 27.73 % 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: -0.21 (0.26), residues: 1001 helix: 0.66 (0.26), residues: 366 sheet: 0.06 (0.39), residues: 174 loop : -0.82 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP h 109 HIS 0.010 0.002 HIS C 104 PHE 0.025 0.003 PHE A 9 TYR 0.052 0.003 TYR A 88 ARG 0.008 0.001 ARG A 98 *********************** 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 380 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 0.917 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 14 GLU cc_start: 0.8458 (mp0) cc_final: 0.7974 (mp0) REVERT: B 57 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8230 (mm-40) REVERT: B 112 ARG cc_start: 0.7756 (tpp-160) cc_final: 0.7350 (tpp-160) REVERT: B 127 ARG cc_start: 0.3172 (tpt170) cc_final: 0.2478 (tmt170) REVERT: A 8 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7319 (tp30) REVERT: A 19 LEU cc_start: 0.8687 (mp) cc_final: 0.8369 (mt) REVERT: A 23 PHE cc_start: 0.4699 (OUTLIER) cc_final: 0.3395 (m-80) REVERT: A 53 THR cc_start: 0.8132 (p) cc_final: 0.7513 (t) REVERT: A 55 LEU cc_start: 0.8801 (tp) cc_final: 0.8455 (tt) REVERT: A 57 GLN cc_start: 0.8546 (mm110) cc_final: 0.8283 (mm110) REVERT: A 66 MET cc_start: 0.7268 (mmt) cc_final: 0.6969 (tpp) REVERT: A 93 MET cc_start: 0.8040 (ttm) cc_final: 0.7777 (ttm) REVERT: A 127 ARG cc_start: 0.4125 (OUTLIER) cc_final: 0.2483 (tmt170) REVERT: D 30 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8316 (tt) REVERT: D 61 CYS cc_start: 0.8706 (t) cc_final: 0.8365 (m) REVERT: C 60 LEU cc_start: 0.8541 (mt) cc_final: 0.8221 (mt) REVERT: C 64 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6965 (mt-10) REVERT: C 87 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7633 (t) REVERT: C 108 LEU cc_start: 0.8186 (mt) cc_final: 0.7919 (mt) REVERT: h 48 LEU cc_start: 0.8362 (mt) cc_final: 0.8134 (mt) REVERT: h 95 PHE cc_start: 0.6299 (m-80) cc_final: 0.5960 (m-80) REVERT: l 31 HIS cc_start: 0.7218 (t-90) cc_final: 0.6952 (t-90) REVERT: l 33 ASN cc_start: 0.8452 (t0) cc_final: 0.8252 (t0) REVERT: l 38 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7406 (m-10) REVERT: H 18 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.6931 (mt) REVERT: H 31 LYS cc_start: 0.8102 (mttt) cc_final: 0.7666 (mmmm) REVERT: H 47 TRP cc_start: 0.7504 (t60) cc_final: 0.7299 (t60) REVERT: H 52 TRP cc_start: 0.7824 (m-10) cc_final: 0.7432 (m-10) REVERT: H 59 ASP cc_start: 0.7971 (t0) cc_final: 0.7683 (t0) REVERT: H 102 ASP cc_start: 0.8296 (t70) cc_final: 0.7900 (t0) REVERT: L 52 LEU cc_start: 0.7790 (mt) cc_final: 0.7493 (mt) outliers start: 68 outliers final: 43 residues processed: 342 average time/residue: 0.1816 time to fit residues: 84.9014 Evaluate side-chains 360 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 310 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER 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 27 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 13 VAL 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 67 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 114 THR 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 37 LEU 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 115 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 13 VAL Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 38 PHE 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 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 21 ILE Chi-restraints excluded: chain L residue 33 ASN 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 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 90 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.136753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.116558 restraints weight = 17563.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120238 restraints weight = 10141.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.122733 restraints weight = 6745.063| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8257 Z= 0.198 Angle : 0.720 10.076 11251 Z= 0.363 Chirality : 0.047 0.340 1230 Planarity : 0.005 0.060 1443 Dihedral : 5.007 58.233 1118 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 5.34 % Allowed : 31.36 % Favored : 63.30 % 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: -0.02 (0.26), residues: 1001 helix: 0.92 (0.26), residues: 370 sheet: -0.20 (0.37), residues: 194 loop : -0.65 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 62 HIS 0.005 0.001 HIS C 104 PHE 0.026 0.002 PHE A 9 TYR 0.064 0.002 TYR A 88 ARG 0.004 0.000 ARG C 56 *********************** 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 347 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8512 (mp0) cc_final: 0.8156 (mp0) REVERT: B 57 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8032 (mm-40) REVERT: B 62 TRP cc_start: 0.8240 (t-100) cc_final: 0.7935 (t-100) REVERT: B 99 GLN cc_start: 0.8585 (mt0) cc_final: 0.8133 (tt0) REVERT: B 112 ARG cc_start: 0.7584 (tpp-160) cc_final: 0.7137 (tpp-160) REVERT: B 127 ARG cc_start: 0.3135 (tpt170) cc_final: 0.2614 (tmt170) REVERT: A 8 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: A 23 PHE cc_start: 0.4486 (OUTLIER) cc_final: 0.3545 (m-80) REVERT: A 53 THR cc_start: 0.7822 (p) cc_final: 0.7164 (t) REVERT: A 57 GLN cc_start: 0.8415 (mm110) cc_final: 0.8167 (mm110) REVERT: A 66 MET cc_start: 0.7252 (mmt) cc_final: 0.6958 (tpp) REVERT: A 93 MET cc_start: 0.8048 (ttm) cc_final: 0.7749 (ttm) REVERT: A 105 ILE cc_start: 0.8975 (tt) cc_final: 0.8743 (tp) REVERT: A 127 ARG cc_start: 0.3649 (OUTLIER) cc_final: 0.2046 (tmt170) REVERT: D 60 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8129 (mm) REVERT: D 61 CYS cc_start: 0.8670 (t) cc_final: 0.8256 (m) REVERT: D 102 TRP cc_start: 0.8693 (t60) cc_final: 0.8052 (t60) REVERT: C 60 LEU cc_start: 0.8428 (mt) cc_final: 0.8058 (mt) REVERT: C 64 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6970 (mt-10) REVERT: C 87 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7548 (t) REVERT: h 13 GLN cc_start: 0.7527 (tm-30) cc_final: 0.6866 (tm-30) REVERT: h 83 MET cc_start: 0.6783 (mpp) cc_final: 0.5873 (mpp) REVERT: h 95 PHE cc_start: 0.6386 (m-80) cc_final: 0.6126 (m-80) REVERT: l 31 HIS cc_start: 0.6960 (t-90) cc_final: 0.6642 (t-90) REVERT: l 38 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7242 (m-10) REVERT: H 18 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7383 (mt) REVERT: H 31 LYS cc_start: 0.8047 (mttt) cc_final: 0.7833 (mttt) REVERT: H 34 MET cc_start: 0.7243 (mmm) cc_final: 0.7033 (mmm) REVERT: H 59 ASP cc_start: 0.7972 (t0) cc_final: 0.7693 (t0) REVERT: H 102 ASP cc_start: 0.8261 (t70) cc_final: 0.7870 (t0) REVERT: L 84 GLU cc_start: 0.7512 (pm20) cc_final: 0.6178 (pm20) outliers start: 47 outliers final: 35 residues processed: 323 average time/residue: 0.1953 time to fit residues: 86.4073 Evaluate side-chains 333 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 66 MET 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 27 ILE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 28 ARG 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 72 VAL Chi-restraints excluded: chain D residue 97 ILE 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 59 ILE 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 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 67 PHE 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 21 ILE Chi-restraints excluded: chain L residue 33 ASN 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 45 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 35 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** l 33 ASN ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.136376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.116055 restraints weight = 17790.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.119772 restraints weight = 10279.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122290 restraints weight = 6824.620| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8257 Z= 0.209 Angle : 0.727 13.677 11251 Z= 0.364 Chirality : 0.046 0.338 1230 Planarity : 0.005 0.059 1443 Dihedral : 4.961 59.895 1118 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 5.23 % Allowed : 32.61 % Favored : 62.16 % 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: 0.03 (0.27), residues: 1001 helix: 0.89 (0.26), residues: 370 sheet: -0.11 (0.38), residues: 194 loop : -0.59 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP H 47 HIS 0.004 0.001 HIS C 104 PHE 0.023 0.002 PHE A 9 TYR 0.067 0.002 TYR A 88 ARG 0.006 0.000 ARG C 56 *********************** 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 340 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8512 (mp0) cc_final: 0.8122 (mp0) REVERT: B 57 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8006 (mm-40) REVERT: B 62 TRP cc_start: 0.8274 (t-100) cc_final: 0.7906 (t-100) REVERT: B 99 GLN cc_start: 0.8608 (mt0) cc_final: 0.8182 (tt0) REVERT: B 112 ARG cc_start: 0.7544 (tpp-160) cc_final: 0.7091 (tpp-160) REVERT: B 127 ARG cc_start: 0.3177 (tpt170) cc_final: 0.2732 (tmt170) REVERT: A 8 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7234 (tp30) REVERT: A 23 PHE cc_start: 0.4399 (OUTLIER) cc_final: 0.3546 (m-80) REVERT: A 39 ARG cc_start: 0.7595 (ttp-110) cc_final: 0.7309 (ttp80) REVERT: A 42 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8170 (mm) REVERT: A 53 THR cc_start: 0.7818 (p) cc_final: 0.7141 (t) REVERT: A 57 GLN cc_start: 0.8426 (mm110) cc_final: 0.8146 (mm110) REVERT: A 66 MET cc_start: 0.7323 (mmt) cc_final: 0.7016 (tpp) REVERT: A 93 MET cc_start: 0.8091 (ttm) cc_final: 0.7800 (ttm) REVERT: A 105 ILE cc_start: 0.9014 (tt) cc_final: 0.8793 (tp) REVERT: A 127 ARG cc_start: 0.3717 (OUTLIER) cc_final: 0.2132 (tmt170) REVERT: D 60 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8162 (mm) REVERT: D 61 CYS cc_start: 0.8637 (t) cc_final: 0.8137 (m) REVERT: D 102 TRP cc_start: 0.8738 (t60) cc_final: 0.8180 (t60) REVERT: D 112 ARG cc_start: 0.7920 (mmt90) cc_final: 0.7672 (mtt-85) REVERT: C 56 ARG cc_start: 0.8287 (mmt180) cc_final: 0.8059 (mmt180) REVERT: C 60 LEU cc_start: 0.8444 (mt) cc_final: 0.8084 (mt) REVERT: C 64 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6969 (mt-10) REVERT: C 87 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7542 (t) REVERT: h 13 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7028 (tm-30) REVERT: h 95 PHE cc_start: 0.6316 (m-80) cc_final: 0.6015 (m-80) REVERT: l 31 HIS cc_start: 0.6982 (t-90) cc_final: 0.6655 (t-90) REVERT: l 38 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7197 (m-10) REVERT: H 18 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7343 (mt) REVERT: H 31 LYS cc_start: 0.8049 (mttt) cc_final: 0.7574 (mmmm) REVERT: H 52 TRP cc_start: 0.7694 (m-10) cc_final: 0.7201 (m-10) REVERT: H 59 ASP cc_start: 0.8005 (t0) cc_final: 0.7693 (t0) REVERT: H 67 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.6008 (mpp-170) REVERT: H 102 ASP cc_start: 0.8301 (t70) cc_final: 0.7896 (t0) outliers start: 46 outliers final: 34 residues processed: 316 average time/residue: 0.1848 time to fit residues: 79.5589 Evaluate side-chains 333 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 93 MET 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 27 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 28 ARG 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 72 VAL Chi-restraints excluded: chain D residue 97 ILE 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 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 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 33 ASN Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 67 ARG 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 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.133993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.113596 restraints weight = 18246.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117350 restraints weight = 10466.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.119862 restraints weight = 6924.678| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8257 Z= 0.290 Angle : 0.767 15.116 11251 Z= 0.390 Chirality : 0.047 0.264 1230 Planarity : 0.006 0.062 1443 Dihedral : 5.156 56.221 1118 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.39 % Favored : 94.51 % Rotamer: Outliers : 5.45 % Allowed : 32.05 % Favored : 62.50 % 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: -0.10 (0.27), residues: 1001 helix: 0.84 (0.27), residues: 371 sheet: -0.21 (0.37), residues: 194 loop : -0.71 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP H 47 HIS 0.005 0.001 HIS C 104 PHE 0.027 0.002 PHE A 9 TYR 0.066 0.002 TYR A 88 ARG 0.008 0.001 ARG A 56 *********************** 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 350 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8551 (mp0) cc_final: 0.8130 (mp0) REVERT: B 57 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8106 (mm-40) REVERT: B 62 TRP cc_start: 0.8312 (t-100) cc_final: 0.7995 (t-100) REVERT: B 99 GLN cc_start: 0.8641 (mt0) cc_final: 0.8205 (tt0) REVERT: B 127 ARG cc_start: 0.3346 (tpt170) cc_final: 0.2770 (tmt170) REVERT: A 8 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 23 PHE cc_start: 0.4411 (OUTLIER) cc_final: 0.3587 (m-80) REVERT: A 42 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8183 (mm) REVERT: A 53 THR cc_start: 0.7903 (p) cc_final: 0.7216 (t) REVERT: A 57 GLN cc_start: 0.8449 (mm110) cc_final: 0.8168 (mm110) REVERT: A 66 MET cc_start: 0.7358 (mmt) cc_final: 0.7055 (tpp) REVERT: A 93 MET cc_start: 0.8093 (ttm) cc_final: 0.7818 (ttm) REVERT: A 105 ILE cc_start: 0.9070 (tt) cc_final: 0.8853 (tp) REVERT: A 127 ARG cc_start: 0.3876 (OUTLIER) cc_final: 0.2246 (tmt170) REVERT: D 60 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8178 (mm) REVERT: D 61 CYS cc_start: 0.8633 (t) cc_final: 0.8140 (m) REVERT: D 62 TRP cc_start: 0.7977 (t-100) cc_final: 0.7741 (t-100) REVERT: D 102 TRP cc_start: 0.8840 (t60) cc_final: 0.7865 (t60) REVERT: C 56 ARG cc_start: 0.8330 (mmt180) cc_final: 0.8083 (mtt-85) REVERT: C 60 LEU cc_start: 0.8492 (mt) cc_final: 0.8144 (mt) REVERT: C 64 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6995 (mt-10) REVERT: C 87 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7576 (t) REVERT: h 48 LEU cc_start: 0.8316 (mt) cc_final: 0.8092 (mt) REVERT: h 95 PHE cc_start: 0.6258 (m-80) cc_final: 0.5887 (m-80) REVERT: l 31 HIS cc_start: 0.7192 (t-90) cc_final: 0.6888 (t-90) REVERT: l 38 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: H 18 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7278 (mt) REVERT: H 31 LYS cc_start: 0.8082 (mttt) cc_final: 0.7609 (mmmm) REVERT: H 36 TRP cc_start: 0.7287 (m100) cc_final: 0.6770 (m100) REVERT: H 50 TYR cc_start: 0.7264 (p90) cc_final: 0.7055 (p90) REVERT: H 52 TRP cc_start: 0.7800 (m-10) cc_final: 0.7363 (m-10) REVERT: H 59 ASP cc_start: 0.8048 (t0) cc_final: 0.7736 (t0) REVERT: H 67 ARG cc_start: 0.6358 (mpp-170) cc_final: 0.5712 (mpp-170) REVERT: H 102 ASP cc_start: 0.8326 (t70) cc_final: 0.8004 (t0) REVERT: L 52 LEU cc_start: 0.7568 (mt) cc_final: 0.7315 (mt) outliers start: 48 outliers final: 37 residues processed: 323 average time/residue: 0.1831 time to fit residues: 80.5578 Evaluate side-chains 347 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 95 LEU 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 27 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 28 ARG 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 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 40 GLU 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 40 VAL Chi-restraints excluded: chain h residue 114 LEU 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 94 MET 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 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 37 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.135468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115529 restraints weight = 17509.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119135 restraints weight = 10219.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121583 restraints weight = 6805.158| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8257 Z= 0.243 Angle : 0.758 13.292 11251 Z= 0.383 Chirality : 0.048 0.388 1230 Planarity : 0.006 0.059 1443 Dihedral : 5.066 55.043 1118 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 5.45 % Allowed : 32.61 % Favored : 61.93 % 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: -0.19 (0.27), residues: 1001 helix: 0.82 (0.26), residues: 371 sheet: -0.19 (0.37), residues: 194 loop : -0.85 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP H 47 HIS 0.004 0.001 HIS C 104 PHE 0.039 0.002 PHE l 103 TYR 0.063 0.002 TYR A 88 ARG 0.007 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 350 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8508 (mp0) cc_final: 0.8096 (mp0) REVERT: B 57 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8052 (mm-40) REVERT: B 62 TRP cc_start: 0.8295 (t-100) cc_final: 0.7980 (t-100) REVERT: B 99 GLN cc_start: 0.8630 (mt0) cc_final: 0.8197 (tt0) REVERT: B 112 ARG cc_start: 0.7556 (tpp-160) cc_final: 0.7117 (tpp-160) REVERT: B 127 ARG cc_start: 0.3378 (tpt170) cc_final: 0.3108 (tpt-90) REVERT: A 8 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: A 23 PHE cc_start: 0.4447 (OUTLIER) cc_final: 0.3723 (m-80) REVERT: A 42 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8252 (mm) REVERT: A 53 THR cc_start: 0.7864 (p) cc_final: 0.7181 (t) REVERT: A 57 GLN cc_start: 0.8409 (mm110) cc_final: 0.8131 (mm110) REVERT: A 66 MET cc_start: 0.7387 (mmt) cc_final: 0.7163 (tpp) REVERT: A 93 MET cc_start: 0.8067 (ttm) cc_final: 0.7816 (ttm) REVERT: A 105 ILE cc_start: 0.9048 (tt) cc_final: 0.8825 (tp) REVERT: A 125 TRP cc_start: 0.8468 (t-100) cc_final: 0.8255 (t-100) REVERT: A 127 ARG cc_start: 0.3901 (OUTLIER) cc_final: 0.2267 (tmt170) REVERT: D 60 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8141 (mm) REVERT: D 61 CYS cc_start: 0.8591 (t) cc_final: 0.8118 (m) REVERT: D 102 TRP cc_start: 0.8827 (t60) cc_final: 0.7903 (t60) REVERT: D 112 ARG cc_start: 0.7990 (mmt90) cc_final: 0.7533 (mtt-85) REVERT: C 60 LEU cc_start: 0.8425 (mt) cc_final: 0.8070 (mt) REVERT: C 64 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 87 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7618 (t) REVERT: h 48 LEU cc_start: 0.8310 (mt) cc_final: 0.8083 (mt) REVERT: h 95 PHE cc_start: 0.6313 (m-80) cc_final: 0.5984 (m-80) REVERT: l 31 HIS cc_start: 0.7101 (t-90) cc_final: 0.6841 (t-90) REVERT: l 33 ASN cc_start: 0.8582 (t0) cc_final: 0.8345 (p0) REVERT: l 38 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: H 18 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7118 (mt) REVERT: H 31 LYS cc_start: 0.8073 (mttt) cc_final: 0.7597 (mmmm) REVERT: H 36 TRP cc_start: 0.7362 (m100) cc_final: 0.6857 (m100) REVERT: H 50 TYR cc_start: 0.7190 (p90) cc_final: 0.6984 (p90) REVERT: H 52 TRP cc_start: 0.7856 (m-10) cc_final: 0.7420 (m-10) REVERT: H 59 ASP cc_start: 0.8037 (t0) cc_final: 0.7731 (t0) REVERT: H 67 ARG cc_start: 0.6532 (mpp-170) cc_final: 0.5891 (mpp-170) REVERT: H 102 ASP cc_start: 0.8389 (t70) cc_final: 0.7999 (t0) REVERT: L 24 ARG cc_start: 0.6099 (tpp-160) cc_final: 0.5881 (tpp-160) REVERT: L 40 TRP cc_start: 0.6069 (m100) cc_final: 0.5179 (m100) outliers start: 48 outliers final: 37 residues processed: 323 average time/residue: 0.1893 time to fit residues: 83.4819 Evaluate side-chains 346 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 301 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 95 LEU 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 27 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 28 ARG 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 115 VAL 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 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 40 VAL Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE 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 94 MET 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 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 5 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.136437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116474 restraints weight = 17659.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120110 restraints weight = 10265.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.122588 restraints weight = 6837.536| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.5947 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= 0.210 Angle : 0.758 13.280 11251 Z= 0.377 Chirality : 0.047 0.366 1230 Planarity : 0.005 0.059 1443 Dihedral : 4.960 54.335 1118 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 5.23 % Allowed : 32.61 % Favored : 62.16 % 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: -0.11 (0.27), residues: 1001 helix: 0.92 (0.27), residues: 368 sheet: -0.16 (0.37), residues: 194 loop : -0.82 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 47 HIS 0.004 0.001 HIS C 104 PHE 0.047 0.002 PHE l 103 TYR 0.061 0.002 TYR A 88 ARG 0.007 0.001 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2840.66 seconds wall clock time: 51 minutes 24.58 seconds (3084.58 seconds total)