Starting phenix.real_space_refine on Wed Sep 17 10:06:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrh_60396/09_2025/8zrh_60396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrh_60396/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zrh_60396/09_2025/8zrh_60396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrh_60396/09_2025/8zrh_60396.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zrh_60396/09_2025/8zrh_60396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrh_60396/09_2025/8zrh_60396.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.29, per 1000 atoms: 0.28 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: 0.60 Conformation dependent library (CDL) restraints added in 489.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.30 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: 1.18 Time building geometry restraints manager: 0.87 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: 0.770 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- 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 8261 Z= 0.498 Angle : 0.928 8.445 11259 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (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 ARG 0.004 0.001 ARG l 97 TYR 0.017 0.002 TYR B 6 PHE 0.029 0.002 PHE B 110 TRP 0.019 0.002 TRP B 102 HIS 0.005 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00712 ( 8257) covalent geometry : angle 0.92750 (11251) SS BOND : bond 0.00614 ( 4) SS BOND : angle 1.52735 ( 8) hydrogen bonds : bond 0.24170 ( 385) hydrogen bonds : angle 8.51652 ( 1068) *********************** 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 : 0.282 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: 0.0856 time to fit residues: 35.2477 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 : 0.295 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.0020 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.152526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.133067 restraints weight = 18178.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.136934 restraints weight = 10374.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.139584 restraints weight = 6745.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.141419 restraints weight = 4738.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.142687 restraints weight = 3555.621| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8261 Z= 0.141 Angle : 0.663 8.419 11259 Z= 0.343 Chirality : 0.043 0.242 1230 Planarity : 0.006 0.057 1443 Dihedral : 4.737 52.337 1122 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.27), residues: 1001 helix: 1.44 (0.27), residues: 363 sheet: 0.29 (0.37), residues: 204 loop : -0.08 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 56 TYR 0.023 0.002 TYR A 88 PHE 0.016 0.002 PHE H 27 TRP 0.019 0.002 TRP B 102 HIS 0.008 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8257) covalent geometry : angle 0.66301 (11251) SS BOND : bond 0.00543 ( 4) SS BOND : angle 1.01164 ( 8) hydrogen bonds : bond 0.05028 ( 385) hydrogen bonds : angle 5.83702 ( 1068) *********************** 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 350 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 0.191 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: 0.8204 (mm-40) cc_final: 0.7942 (mm-40) REVERT: B 62 TRP cc_start: 0.8052 (t-100) cc_final: 0.7816 (t-100) REVERT: B 93 MET cc_start: 0.7790 (mtp) cc_final: 0.7516 (mtm) REVERT: A 107 CYS cc_start: 0.8061 (t) cc_final: 0.7491 (t) REVERT: C 57 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: C 64 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6750 (mt-10) REVERT: C 83 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: h 7 SER cc_start: 0.6816 (m) cc_final: 0.6480 (t) REVERT: h 19 ARG cc_start: 0.8203 (ptm160) cc_final: 0.7906 (ptp-170) REVERT: h 64 VAL cc_start: 0.7233 (m) cc_final: 0.6919 (p) REVERT: h 83 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.5784 (mpp) REVERT: H 31 LYS cc_start: 0.7843 (mttt) cc_final: 0.7612 (mttt) REVERT: H 50 TYR cc_start: 0.7310 (p90) cc_final: 0.7109 (p90) REVERT: H 108 SER cc_start: 0.7977 (p) cc_final: 0.7765 (p) outliers start: 53 outliers final: 26 residues processed: 317 average time/residue: 0.0851 time to fit residues: 36.8785 Evaluate side-chains 303 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 273 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 64 GLU 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 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 L 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.143993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.124258 restraints weight = 17734.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.128072 restraints weight = 10306.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130684 restraints weight = 6774.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.132517 restraints weight = 4836.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.133811 restraints weight = 3662.373| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8261 Z= 0.132 Angle : 0.641 11.155 11259 Z= 0.324 Chirality : 0.042 0.225 1230 Planarity : 0.005 0.056 1443 Dihedral : 4.455 49.739 1118 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer: Outliers : 5.57 % Allowed : 24.77 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 1001 helix: 1.59 (0.27), residues: 362 sheet: 0.16 (0.36), residues: 212 loop : -0.04 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 56 TYR 0.043 0.002 TYR A 88 PHE 0.020 0.002 PHE B 23 TRP 0.024 0.002 TRP H 109 HIS 0.019 0.002 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8257) covalent geometry : angle 0.64057 (11251) SS BOND : bond 0.00512 ( 4) SS BOND : angle 0.86074 ( 8) hydrogen bonds : bond 0.04419 ( 385) hydrogen bonds : angle 5.29791 ( 1068) *********************** 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 325 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 276 time to evaluate : 0.333 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: 0.8142 (mm-40) cc_final: 0.7934 (mm-40) REVERT: B 62 TRP cc_start: 0.8075 (t-100) cc_final: 0.7851 (t-100) REVERT: B 93 MET cc_start: 0.7808 (mtp) cc_final: 0.7398 (mtm) REVERT: A 72 VAL cc_start: 0.8403 (t) cc_final: 0.8187 (p) REVERT: D 61 CYS cc_start: 0.8760 (t) cc_final: 0.8294 (m) REVERT: D 102 TRP cc_start: 0.8279 (t-100) cc_final: 0.8032 (t-100) REVERT: C 57 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: C 83 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: C 118 TYR cc_start: 0.7424 (t80) cc_final: 0.6752 (t80) REVERT: h 7 SER cc_start: 0.6782 (m) cc_final: 0.6453 (t) REVERT: h 13 GLN cc_start: 0.7629 (tm-30) cc_final: 0.6988 (tm-30) REVERT: h 64 VAL cc_start: 0.7245 (m) cc_final: 0.6960 (p) REVERT: h 95 PHE cc_start: 0.6403 (m-80) cc_final: 0.6139 (m-80) REVERT: l 29 LEU cc_start: 0.8314 (mt) cc_final: 0.7754 (mt) REVERT: l 31 HIS cc_start: 0.6795 (t-90) cc_final: 0.6303 (t-90) REVERT: l 33 ASN cc_start: 0.8287 (t0) cc_final: 0.8063 (t0) REVERT: H 18 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7930 (mt) REVERT: L 59 ARG cc_start: 0.8077 (mtt180) cc_final: 0.7813 (mtt180) REVERT: L 84 GLU cc_start: 0.7270 (pm20) cc_final: 0.6477 (pm20) outliers start: 49 outliers final: 31 residues processed: 294 average time/residue: 0.0780 time to fit residues: 31.7637 Evaluate side-chains 301 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 LEU 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 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 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 55 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 101 LEU 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 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 90 VAL Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 2 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 52 HIS ** D 99 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 = 0.4068 r_free = 0.4068 target = 0.144907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.124778 restraints weight = 18194.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128671 restraints weight = 10519.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131312 restraints weight = 6924.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.133152 restraints weight = 4974.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.134438 restraints weight = 3799.733| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8261 Z= 0.134 Angle : 0.638 10.564 11259 Z= 0.320 Chirality : 0.042 0.227 1230 Planarity : 0.005 0.059 1443 Dihedral : 4.447 49.678 1118 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 5.00 % Allowed : 26.82 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 1001 helix: 1.55 (0.27), residues: 362 sheet: 0.44 (0.37), residues: 192 loop : -0.15 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 56 TYR 0.052 0.002 TYR A 88 PHE 0.027 0.002 PHE D 24 TRP 0.021 0.002 TRP H 47 HIS 0.011 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8257) covalent geometry : angle 0.63782 (11251) SS BOND : bond 0.00507 ( 4) SS BOND : angle 0.74871 ( 8) hydrogen bonds : bond 0.04245 ( 385) hydrogen bonds : angle 5.09636 ( 1068) *********************** 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 325 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 0.244 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: 0.8183 (mm-40) cc_final: 0.7928 (mm-40) REVERT: A 39 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.7274 (ttp-110) REVERT: A 53 THR cc_start: 0.7511 (p) cc_final: 0.7050 (t) REVERT: A 55 LEU cc_start: 0.8657 (tp) cc_final: 0.8287 (tt) REVERT: A 107 CYS cc_start: 0.7595 (t) cc_final: 0.7072 (t) REVERT: D 61 CYS cc_start: 0.8649 (t) cc_final: 0.8164 (m) REVERT: D 102 TRP cc_start: 0.8305 (t-100) cc_final: 0.8082 (t-100) REVERT: C 83 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6012 (mp0) REVERT: C 118 TYR cc_start: 0.7622 (t80) cc_final: 0.7185 (t80) REVERT: h 7 SER cc_start: 0.6798 (m) cc_final: 0.6458 (t) REVERT: h 13 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7116 (tm-30) REVERT: h 64 VAL cc_start: 0.7190 (m) cc_final: 0.6919 (p) REVERT: h 95 PHE cc_start: 0.6394 (m-80) cc_final: 0.6149 (m-80) REVERT: l 31 HIS cc_start: 0.6789 (t-90) cc_final: 0.6315 (t-90) REVERT: l 33 ASN cc_start: 0.8359 (t0) cc_final: 0.8098 (t0) REVERT: l 38 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: L 84 GLU cc_start: 0.7179 (pm20) cc_final: 0.6114 (pm20) outliers start: 44 outliers final: 33 residues processed: 296 average time/residue: 0.0762 time to fit residues: 31.3663 Evaluate side-chains 302 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 267 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 105 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 99 THR 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 85 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.141824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.121645 restraints weight = 18114.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.125492 restraints weight = 10416.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.128068 restraints weight = 6861.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129853 restraints weight = 4942.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131099 restraints weight = 3781.050| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8261 Z= 0.138 Angle : 0.648 11.769 11259 Z= 0.322 Chirality : 0.043 0.225 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.465 49.423 1118 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 5.34 % Allowed : 27.50 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.27), residues: 1001 helix: 1.42 (0.27), residues: 364 sheet: 0.20 (0.37), residues: 202 loop : -0.11 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 59 TYR 0.047 0.002 TYR A 88 PHE 0.023 0.002 PHE D 24 TRP 0.026 0.002 TRP H 47 HIS 0.014 0.002 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8257) covalent geometry : angle 0.64836 (11251) SS BOND : bond 0.00488 ( 4) SS BOND : angle 0.67916 ( 8) hydrogen bonds : bond 0.04247 ( 385) hydrogen bonds : angle 5.01063 ( 1068) *********************** 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 328 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 0.381 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: 0.8225 (mm-40) cc_final: 0.7954 (mm-40) REVERT: B 62 TRP cc_start: 0.8124 (t-100) cc_final: 0.7746 (t-100) REVERT: A 9 PHE cc_start: 0.7327 (m-80) cc_final: 0.6898 (m-10) REVERT: A 53 THR cc_start: 0.7540 (p) cc_final: 0.6958 (t) REVERT: A 107 CYS cc_start: 0.7803 (t) cc_final: 0.7199 (t) REVERT: D 61 CYS cc_start: 0.8648 (t) cc_final: 0.8174 (m) REVERT: C 64 GLU cc_start: 0.7155 (tt0) cc_final: 0.6817 (mt-10) REVERT: C 72 VAL cc_start: 0.8996 (t) cc_final: 0.8755 (p) REVERT: C 83 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: C 84 LEU cc_start: 0.8042 (mt) cc_final: 0.7823 (mt) REVERT: C 87 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.7257 (p) REVERT: h 7 SER cc_start: 0.6859 (m) cc_final: 0.6460 (t) REVERT: h 13 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7107 (tm-30) REVERT: h 64 VAL cc_start: 0.7181 (m) cc_final: 0.6935 (p) REVERT: h 95 PHE cc_start: 0.6379 (m-80) cc_final: 0.6125 (m-80) REVERT: l 31 HIS cc_start: 0.6804 (t-90) cc_final: 0.6324 (t-90) REVERT: l 33 ASN cc_start: 0.8415 (t0) cc_final: 0.8126 (t0) REVERT: l 38 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: H 18 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7898 (mt) REVERT: H 36 TRP cc_start: 0.6875 (m100) cc_final: 0.6637 (m100) REVERT: H 59 ASP cc_start: 0.7907 (t0) cc_final: 0.7644 (t0) REVERT: L 59 ARG cc_start: 0.8328 (mtt180) cc_final: 0.8096 (mtp180) REVERT: L 84 GLU cc_start: 0.7290 (pm20) cc_final: 0.6102 (pm20) outliers start: 47 outliers final: 38 residues processed: 298 average time/residue: 0.0810 time to fit residues: 33.4267 Evaluate side-chains 316 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 114 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 51 HIS 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 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 55 LEU 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 101 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 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 64 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 51 HIS ** 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 = 0.4037 r_free = 0.4037 target = 0.142698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.122544 restraints weight = 17857.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.126291 restraints weight = 10427.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.128829 restraints weight = 6949.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.130577 restraints weight = 5042.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.131805 restraints weight = 3900.736| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8261 Z= 0.120 Angle : 0.648 10.050 11259 Z= 0.317 Chirality : 0.043 0.287 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.355 49.572 1118 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 5.68 % Allowed : 29.89 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.27), residues: 1001 helix: 1.40 (0.27), residues: 365 sheet: 0.23 (0.37), residues: 202 loop : -0.08 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 67 TYR 0.047 0.001 TYR A 88 PHE 0.022 0.002 PHE H 95 TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8257) covalent geometry : angle 0.64790 (11251) SS BOND : bond 0.00470 ( 4) SS BOND : angle 0.67998 ( 8) hydrogen bonds : bond 0.03928 ( 385) hydrogen bonds : angle 4.89475 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 277 time to evaluate : 0.231 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: 0.8192 (mp0) cc_final: 0.7985 (mp0) REVERT: B 57 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7909 (mm-40) REVERT: A 8 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7049 (tp30) REVERT: A 127 ARG cc_start: 0.3432 (OUTLIER) cc_final: 0.2033 (tmt170) REVERT: D 60 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8069 (mm) REVERT: D 61 CYS cc_start: 0.8686 (t) cc_final: 0.8209 (m) REVERT: D 97 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7762 (tt) REVERT: C 64 GLU cc_start: 0.7177 (tt0) cc_final: 0.6848 (mt-10) REVERT: C 72 VAL cc_start: 0.8987 (t) cc_final: 0.8761 (p) REVERT: C 83 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: C 118 TYR cc_start: 0.7726 (t80) cc_final: 0.7522 (t80) REVERT: h 7 SER cc_start: 0.6866 (m) cc_final: 0.6448 (t) REVERT: h 13 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7068 (tm-30) REVERT: h 64 VAL cc_start: 0.7188 (m) cc_final: 0.6948 (p) REVERT: h 95 PHE cc_start: 0.6335 (m-80) cc_final: 0.6059 (m-80) REVERT: l 31 HIS cc_start: 0.6873 (t-90) cc_final: 0.6398 (t-90) REVERT: l 33 ASN cc_start: 0.8444 (t0) cc_final: 0.8196 (t0) REVERT: l 38 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: H 18 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7904 (mt) REVERT: H 59 ASP cc_start: 0.7889 (t0) cc_final: 0.7635 (t0) REVERT: L 84 GLU cc_start: 0.7381 (pm20) cc_final: 0.6357 (pm20) REVERT: L 108 LYS cc_start: 0.7501 (tppt) cc_final: 0.7283 (tppt) outliers start: 50 outliers final: 32 residues processed: 298 average time/residue: 0.0810 time to fit residues: 33.3117 Evaluate side-chains 304 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 114 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 ILE 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 55 LEU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 HIS h 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.144629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124270 restraints weight = 17817.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.127940 restraints weight = 10448.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.130392 restraints weight = 7007.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132092 restraints weight = 5134.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.133329 restraints weight = 4025.147| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8261 Z= 0.120 Angle : 0.665 14.099 11259 Z= 0.321 Chirality : 0.043 0.262 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.347 50.486 1118 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 6.02 % Allowed : 29.77 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.27), residues: 1001 helix: 1.34 (0.27), residues: 372 sheet: 0.39 (0.37), residues: 188 loop : -0.34 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 56 TYR 0.050 0.002 TYR A 88 PHE 0.023 0.002 PHE C 23 TRP 0.023 0.002 TRP H 47 HIS 0.003 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8257) covalent geometry : angle 0.66527 (11251) SS BOND : bond 0.00517 ( 4) SS BOND : angle 0.87451 ( 8) hydrogen bonds : bond 0.03849 ( 385) hydrogen bonds : angle 4.85710 ( 1068) *********************** 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 323 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8224 (mp0) cc_final: 0.7998 (mp0) REVERT: B 57 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7887 (mm-40) REVERT: A 8 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: A 23 PHE cc_start: 0.3909 (OUTLIER) cc_final: 0.2981 (m-80) REVERT: A 127 ARG cc_start: 0.3675 (OUTLIER) cc_final: 0.2233 (tmt170) REVERT: D 60 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8068 (mm) REVERT: D 61 CYS cc_start: 0.8645 (t) cc_final: 0.8148 (m) REVERT: D 97 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7807 (tt) REVERT: C 64 GLU cc_start: 0.7200 (tt0) cc_final: 0.6851 (mt-10) REVERT: C 72 VAL cc_start: 0.9019 (t) cc_final: 0.8798 (p) REVERT: h 7 SER cc_start: 0.6888 (m) cc_final: 0.6461 (t) REVERT: h 13 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7068 (tm-30) REVERT: h 64 VAL cc_start: 0.7195 (m) cc_final: 0.6950 (p) REVERT: h 95 PHE cc_start: 0.6304 (m-80) cc_final: 0.6054 (m-80) REVERT: h 109 TRP cc_start: 0.7358 (m-10) cc_final: 0.7131 (m-10) REVERT: l 31 HIS cc_start: 0.6909 (t-90) cc_final: 0.6411 (t-90) REVERT: l 33 ASN cc_start: 0.8504 (t0) cc_final: 0.8251 (t0) REVERT: l 38 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7173 (m-10) REVERT: H 18 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7714 (mt) REVERT: H 59 ASP cc_start: 0.7927 (t0) cc_final: 0.7661 (t0) REVERT: L 84 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6434 (pm20) outliers start: 53 outliers final: 38 residues processed: 299 average time/residue: 0.0785 time to fit residues: 32.5993 Evaluate side-chains 318 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ILE 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 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 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 55 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 26 SER Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain 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 7 SER Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 0.0070 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.144148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.124011 restraints weight = 17751.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.127798 restraints weight = 10194.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.130336 restraints weight = 6728.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.132110 restraints weight = 4859.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.133352 restraints weight = 3744.353| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8261 Z= 0.118 Angle : 0.681 12.382 11259 Z= 0.327 Chirality : 0.043 0.290 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.332 51.439 1118 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 4.89 % Allowed : 31.36 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.27), residues: 1001 helix: 1.30 (0.27), residues: 371 sheet: 0.27 (0.38), residues: 194 loop : -0.11 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 56 TYR 0.053 0.002 TYR A 88 PHE 0.031 0.002 PHE H 68 TRP 0.030 0.002 TRP B 71 HIS 0.007 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8257) covalent geometry : angle 0.68050 (11251) SS BOND : bond 0.00599 ( 4) SS BOND : angle 0.97463 ( 8) hydrogen bonds : bond 0.03816 ( 385) hydrogen bonds : angle 4.81423 ( 1068) *********************** 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 319 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 276 time to evaluate : 0.300 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: 0.8268 (mp0) cc_final: 0.8017 (mp0) REVERT: B 57 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7925 (mm-40) REVERT: B 93 MET cc_start: 0.7473 (ptp) cc_final: 0.7238 (ptp) REVERT: B 99 GLN cc_start: 0.8563 (mt0) cc_final: 0.8050 (tt0) REVERT: A 8 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7048 (tp30) REVERT: A 23 PHE cc_start: 0.3862 (OUTLIER) cc_final: 0.2831 (m-80) REVERT: A 127 ARG cc_start: 0.3600 (OUTLIER) cc_final: 0.2149 (tmt170) REVERT: D 60 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8050 (mm) REVERT: D 61 CYS cc_start: 0.8659 (t) cc_final: 0.8125 (m) REVERT: C 64 GLU cc_start: 0.7196 (tt0) cc_final: 0.6838 (mt-10) REVERT: C 72 VAL cc_start: 0.8992 (t) cc_final: 0.8768 (p) REVERT: C 93 MET cc_start: 0.7957 (ttm) cc_final: 0.7676 (ptp) REVERT: h 7 SER cc_start: 0.6894 (m) cc_final: 0.6457 (t) REVERT: h 13 GLN cc_start: 0.7640 (tm-30) cc_final: 0.6962 (tm-30) REVERT: h 64 VAL cc_start: 0.7200 (m) cc_final: 0.6959 (p) REVERT: h 95 PHE cc_start: 0.6302 (m-80) cc_final: 0.6057 (m-80) REVERT: h 109 TRP cc_start: 0.7431 (m-10) cc_final: 0.7222 (m-10) REVERT: l 38 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: H 18 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7805 (mt) REVERT: H 59 ASP cc_start: 0.7958 (t0) cc_final: 0.7679 (t0) REVERT: L 59 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7994 (mtt180) REVERT: L 84 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6410 (pm20) outliers start: 43 outliers final: 30 residues processed: 294 average time/residue: 0.0780 time to fit residues: 31.7313 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 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 55 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.141968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121666 restraints weight = 17798.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.125316 restraints weight = 10405.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127830 restraints weight = 6973.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129532 restraints weight = 5094.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.130763 restraints weight = 3977.082| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8261 Z= 0.138 Angle : 0.682 11.147 11259 Z= 0.337 Chirality : 0.044 0.193 1230 Planarity : 0.005 0.061 1443 Dihedral : 4.492 53.434 1118 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 4.32 % Allowed : 31.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.27), residues: 1001 helix: 1.24 (0.27), residues: 371 sheet: 0.19 (0.37), residues: 194 loop : -0.24 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 67 TYR 0.049 0.002 TYR A 88 PHE 0.052 0.002 PHE H 68 TRP 0.038 0.003 TRP D 102 HIS 0.006 0.001 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8257) covalent geometry : angle 0.68055 (11251) SS BOND : bond 0.00889 ( 4) SS BOND : angle 1.68486 ( 8) hydrogen bonds : bond 0.04251 ( 385) hydrogen bonds : angle 4.82996 ( 1068) *********************** 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 321 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 283 time to evaluate : 0.289 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: 0.8189 (mm-40) cc_final: 0.7924 (mm-40) REVERT: B 62 TRP cc_start: 0.8131 (t-100) cc_final: 0.7918 (t-100) REVERT: B 93 MET cc_start: 0.7496 (ptp) cc_final: 0.7065 (ptp) REVERT: B 99 GLN cc_start: 0.8601 (mt0) cc_final: 0.8106 (tt0) REVERT: A 8 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7060 (tp30) REVERT: A 23 PHE cc_start: 0.3958 (OUTLIER) cc_final: 0.2910 (m-80) REVERT: A 93 MET cc_start: 0.7996 (ttm) cc_final: 0.7719 (ttm) REVERT: A 105 ILE cc_start: 0.8935 (tp) cc_final: 0.8563 (tp) REVERT: A 127 ARG cc_start: 0.3647 (OUTLIER) cc_final: 0.2216 (tmt170) REVERT: D 60 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (mm) REVERT: D 61 CYS cc_start: 0.8603 (t) cc_final: 0.8095 (m) REVERT: C 64 GLU cc_start: 0.7295 (tt0) cc_final: 0.6906 (mt-10) REVERT: C 72 VAL cc_start: 0.9067 (t) cc_final: 0.8866 (p) REVERT: C 93 MET cc_start: 0.7967 (ttm) cc_final: 0.7736 (ptp) REVERT: C 118 TYR cc_start: 0.7680 (t80) cc_final: 0.7059 (t80) REVERT: h 7 SER cc_start: 0.6970 (m) cc_final: 0.6524 (t) REVERT: h 13 GLN cc_start: 0.7634 (tm-30) cc_final: 0.6943 (tm-30) REVERT: h 64 VAL cc_start: 0.7143 (m) cc_final: 0.6909 (p) REVERT: h 95 PHE cc_start: 0.6278 (m-80) cc_final: 0.6023 (m-80) REVERT: l 27 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7822 (tm-30) REVERT: l 33 ASN cc_start: 0.8576 (t0) cc_final: 0.8206 (p0) REVERT: l 38 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7267 (m-10) REVERT: H 59 ASP cc_start: 0.7995 (t0) cc_final: 0.7713 (t0) REVERT: L 59 ARG cc_start: 0.8318 (mtt180) cc_final: 0.8095 (mtt180) REVERT: L 84 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6221 (pm20) outliers start: 38 outliers final: 29 residues processed: 299 average time/residue: 0.0800 time to fit residues: 33.0096 Evaluate side-chains 312 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 23 PHE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 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 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 h residue 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 84 GLU 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 61 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 65 optimal weight: 0.0980 chunk 44 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.142303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122230 restraints weight = 17814.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.126015 restraints weight = 10183.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.128548 restraints weight = 6699.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.130247 restraints weight = 4840.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.131515 restraints weight = 3754.549| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8261 Z= 0.123 Angle : 0.710 12.005 11259 Z= 0.344 Chirality : 0.046 0.418 1230 Planarity : 0.005 0.059 1443 Dihedral : 4.453 53.751 1118 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 3.98 % Allowed : 32.39 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.27), residues: 1001 helix: 1.22 (0.27), residues: 371 sheet: 0.38 (0.38), residues: 184 loop : -0.24 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.052 0.001 TYR A 88 PHE 0.061 0.002 PHE H 68 TRP 0.033 0.003 TRP H 47 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8257) covalent geometry : angle 0.70927 (11251) SS BOND : bond 0.00705 ( 4) SS BOND : angle 1.16951 ( 8) hydrogen bonds : bond 0.03947 ( 385) hydrogen bonds : angle 4.82262 ( 1068) ********************** 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 308 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 0.296 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 7 LYS cc_start: 0.7873 (ttpp) cc_final: 0.7665 (ttpp) REVERT: B 51 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.7163 (m170) REVERT: B 57 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7948 (mm-40) REVERT: B 62 TRP cc_start: 0.8087 (t-100) cc_final: 0.7887 (t-100) REVERT: B 93 MET cc_start: 0.7466 (ptp) cc_final: 0.7002 (ptp) REVERT: B 99 GLN cc_start: 0.8581 (mt0) cc_final: 0.8104 (tt0) REVERT: B 127 ARG cc_start: 0.3284 (tpt170) cc_final: 0.2914 (tmt170) REVERT: A 8 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: A 23 PHE cc_start: 0.3987 (OUTLIER) cc_final: 0.3034 (m-80) REVERT: A 53 THR cc_start: 0.7537 (p) cc_final: 0.7110 (t) REVERT: A 93 MET cc_start: 0.8093 (ttm) cc_final: 0.7806 (ttm) REVERT: A 127 ARG cc_start: 0.3597 (OUTLIER) cc_final: 0.2088 (tmt170) REVERT: D 60 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8029 (mm) REVERT: D 61 CYS cc_start: 0.8593 (t) cc_final: 0.8064 (m) REVERT: C 64 GLU cc_start: 0.7308 (tt0) cc_final: 0.6908 (mt-10) REVERT: C 72 VAL cc_start: 0.9025 (t) cc_final: 0.8819 (p) REVERT: h 7 SER cc_start: 0.6908 (m) cc_final: 0.6469 (t) REVERT: h 13 GLN cc_start: 0.7564 (tm-30) cc_final: 0.6861 (tm-30) REVERT: h 64 VAL cc_start: 0.7161 (m) cc_final: 0.6922 (p) REVERT: h 95 PHE cc_start: 0.6298 (m-80) cc_final: 0.6051 (m-80) REVERT: l 27 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7834 (tm-30) REVERT: l 33 ASN cc_start: 0.8646 (t0) cc_final: 0.8296 (p0) REVERT: l 38 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7276 (m-10) REVERT: H 59 ASP cc_start: 0.8041 (t0) cc_final: 0.7727 (t0) REVERT: L 59 ARG cc_start: 0.8250 (mtt180) cc_final: 0.8030 (mtt180) REVERT: L 84 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6220 (pm20) outliers start: 35 outliers final: 26 residues processed: 287 average time/residue: 0.0835 time to fit residues: 32.7401 Evaluate side-chains 303 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 23 PHE Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 51 HIS 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 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 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 16 ARG Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 84 GLU 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 78 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.122167 restraints weight = 17763.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.125927 restraints weight = 10199.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128484 restraints weight = 6723.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.130249 restraints weight = 4844.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.131465 restraints weight = 3731.845| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8261 Z= 0.122 Angle : 0.688 12.169 11259 Z= 0.337 Chirality : 0.046 0.379 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.459 55.187 1118 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 4.09 % Allowed : 31.48 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.27), residues: 1001 helix: 1.25 (0.27), residues: 370 sheet: 0.10 (0.38), residues: 192 loop : -0.15 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 24 TYR 0.055 0.002 TYR A 88 PHE 0.052 0.002 PHE H 68 TRP 0.033 0.003 TRP H 47 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8257) covalent geometry : angle 0.68800 (11251) SS BOND : bond 0.00732 ( 4) SS BOND : angle 1.10876 ( 8) hydrogen bonds : bond 0.03857 ( 385) hydrogen bonds : angle 4.76797 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.21 seconds wall clock time: 27 minutes 44.61 seconds (1664.61 seconds total)