Starting phenix.real_space_refine on Mon Apr 28 18:59:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrh_60396/04_2025/8zrh_60396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrh_60396/04_2025/8zrh_60396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zrh_60396/04_2025/8zrh_60396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrh_60396/04_2025/8zrh_60396.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrh_60396/04_2025/8zrh_60396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrh_60396/04_2025/8zrh_60396.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5151 2.51 5 N 1357 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8036 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1111 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "A" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1119 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 11, 'TRANS': 128} Chain: "D" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1045 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 10, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1119 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 11, 'TRANS': 128} Chain: "h" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "l" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 880 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 106} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "L" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 880 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 106} Time building chain proxies: 4.84, per 1000 atoms: 0.60 Number of scatterers: 8036 At special positions: 0 Unit cell: (110.622, 120.288, 123.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1493 8.00 N 1357 7.00 C 5151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.04 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 44.6% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 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: 1.90 Time building geometry restraints manager: 2.20 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: 0.550 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.380 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1001 helix: 0.89 (0.27), residues: 346 sheet: 1.00 (0.42), residues: 162 loop : -0.30 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 102 HIS 0.005 0.001 HIS A 104 PHE 0.029 0.002 PHE B 110 TYR 0.017 0.002 TYR B 6 ARG 0.004 0.001 ARG l 97 Details of bonding type rmsd hydrogen bonds : bond 0.24170 ( 385) hydrogen bonds : angle 8.51652 ( 1068) SS BOND : bond 0.00614 ( 4) SS BOND : angle 1.52735 ( 8) covalent geometry : bond 0.00712 ( 8257) covalent geometry : angle 0.92750 (11251) *********************** 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 : 0.793 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: 0.1886 time to fit residues: 76.8644 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 : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain h residue 106 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 HIS D 51 HIS ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.151885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.132501 restraints weight = 17915.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.136344 restraints weight = 10261.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138890 restraints weight = 6653.278| |-----------------------------------------------------------------------------| r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8261 Z= 0.142 Angle : 0.667 8.527 11259 Z= 0.345 Chirality : 0.043 0.241 1230 Planarity : 0.006 0.059 1443 Dihedral : 4.765 52.302 1122 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 6.02 % Allowed : 23.30 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1001 helix: 1.42 (0.27), residues: 363 sheet: 0.30 (0.37), residues: 204 loop : -0.08 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 102 HIS 0.007 0.002 HIS D 51 PHE 0.018 0.002 PHE H 27 TYR 0.022 0.002 TYR A 88 ARG 0.004 0.001 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.05171 ( 385) hydrogen bonds : angle 5.87570 ( 1068) SS BOND : bond 0.00559 ( 4) SS BOND : angle 1.08057 ( 8) covalent geometry : bond 0.00301 ( 8257) covalent geometry : angle 0.66657 (11251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 296 time to evaluate : 0.796 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: 0.8212 (mm-40) cc_final: 0.7929 (mm-40) REVERT: B 62 TRP cc_start: 0.8096 (t-100) cc_final: 0.7881 (t-100) REVERT: B 93 MET cc_start: 0.7837 (mtp) cc_final: 0.7355 (mtm) REVERT: B 112 ARG cc_start: 0.7351 (tpp-160) cc_final: 0.7147 (mmt-90) REVERT: A 107 CYS cc_start: 0.8075 (t) cc_final: 0.7503 (t) REVERT: C 57 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: C 83 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5984 (mp0) REVERT: C 101 LEU cc_start: 0.8632 (mm) cc_final: 0.8430 (mm) REVERT: h 7 SER cc_start: 0.6726 (m) cc_final: 0.6390 (t) REVERT: h 19 ARG cc_start: 0.8217 (ptm160) cc_final: 0.7855 (ptp-170) REVERT: h 64 VAL cc_start: 0.7253 (m) cc_final: 0.6937 (p) REVERT: h 83 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.5900 (mpp) REVERT: H 31 LYS cc_start: 0.7873 (mttt) cc_final: 0.7631 (mttt) REVERT: H 50 TYR cc_start: 0.7352 (p90) cc_final: 0.7151 (p90) REVERT: H 108 SER cc_start: 0.8052 (p) cc_final: 0.7832 (p) outliers start: 53 outliers final: 27 residues processed: 317 average time/residue: 0.1749 time to fit residues: 75.4512 Evaluate side-chains 300 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain h residue 83 MET Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 68 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.0770 chunk 60 optimal weight: 0.3980 chunk 83 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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** l 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.149068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.129308 restraints weight = 17987.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.133150 restraints weight = 10430.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135775 restraints weight = 6856.089| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 0.038 8261 Z= 0.127 Angle : 0.640 11.133 11259 Z= 0.321 Chirality : 0.042 0.191 1230 Planarity : 0.005 0.056 1443 Dihedral : 4.453 49.381 1118 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 5.23 % Allowed : 25.91 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1001 helix: 1.57 (0.27), residues: 363 sheet: 0.12 (0.36), residues: 212 loop : -0.08 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 109 HIS 0.014 0.001 HIS D 51 PHE 0.018 0.002 PHE B 23 TYR 0.043 0.002 TYR A 88 ARG 0.005 0.000 ARG L 66 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 385) hydrogen bonds : angle 5.30240 ( 1068) SS BOND : bond 0.00478 ( 4) SS BOND : angle 0.76030 ( 8) covalent geometry : bond 0.00273 ( 8257) covalent geometry : angle 0.64015 (11251) *********************** 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 318 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 0.960 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: 0.8156 (mm-40) cc_final: 0.7949 (mm-40) REVERT: B 62 TRP cc_start: 0.8084 (t-100) cc_final: 0.7835 (t-100) REVERT: B 93 MET cc_start: 0.7796 (mtp) cc_final: 0.7293 (mtt) REVERT: A 72 VAL cc_start: 0.8448 (t) cc_final: 0.8221 (p) REVERT: D 61 CYS cc_start: 0.8772 (t) cc_final: 0.8360 (m) REVERT: D 102 TRP cc_start: 0.8283 (t-100) cc_final: 0.8037 (t-100) REVERT: C 57 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: C 83 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6005 (mp0) REVERT: C 118 TYR cc_start: 0.7239 (t80) cc_final: 0.6752 (t80) REVERT: h 7 SER cc_start: 0.6779 (m) cc_final: 0.6475 (t) REVERT: h 13 GLN cc_start: 0.7571 (tm-30) cc_final: 0.6879 (tm-30) REVERT: h 64 VAL cc_start: 0.7285 (m) cc_final: 0.6983 (p) REVERT: h 95 PHE cc_start: 0.6371 (m-80) cc_final: 0.6153 (m-80) REVERT: l 29 LEU cc_start: 0.8328 (mt) cc_final: 0.7749 (mt) REVERT: l 31 HIS cc_start: 0.6811 (t-90) cc_final: 0.6297 (t-90) REVERT: l 33 ASN cc_start: 0.8268 (t0) cc_final: 0.7992 (t0) REVERT: l 38 PHE cc_start: 0.7289 (t80) cc_final: 0.7087 (m-80) REVERT: H 18 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7900 (mt) REVERT: L 84 GLU cc_start: 0.7321 (pm20) cc_final: 0.6401 (pm20) outliers start: 46 outliers final: 31 residues processed: 294 average time/residue: 0.1887 time to fit residues: 76.2326 Evaluate side-chains 299 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 89 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 51 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain C residue 6 TYR 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 h residue 84 ASN Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** D 99 GLN ** 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 = 0.4085 r_free = 0.4085 target = 0.148033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.128210 restraints weight = 18024.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.132005 restraints weight = 10381.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.134647 restraints weight = 6827.284| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8261 Z= 0.128 Angle : 0.648 13.445 11259 Z= 0.322 Chirality : 0.042 0.216 1230 Planarity : 0.005 0.058 1443 Dihedral : 4.447 49.270 1118 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.20 % Favored : 96.70 % Rotamer: Outliers : 4.77 % Allowed : 27.39 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1001 helix: 1.55 (0.27), residues: 362 sheet: 0.75 (0.37), residues: 168 loop : -0.33 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.005 0.001 HIS A 51 PHE 0.028 0.002 PHE D 24 TYR 0.053 0.002 TYR A 88 ARG 0.003 0.000 ARG L 59 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 385) hydrogen bonds : angle 5.07099 ( 1068) SS BOND : bond 0.00448 ( 4) SS BOND : angle 0.71824 ( 8) covalent geometry : bond 0.00279 ( 8257) covalent geometry : angle 0.64824 (11251) *********************** 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 307 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 0.869 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: 0.8167 (mm-40) cc_final: 0.7942 (mm-40) REVERT: B 93 MET cc_start: 0.7819 (mtp) cc_final: 0.7410 (mtm) REVERT: A 8 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: A 107 CYS cc_start: 0.7592 (t) cc_final: 0.7084 (t) REVERT: A 108 LEU cc_start: 0.8480 (pp) cc_final: 0.8209 (pp) REVERT: D 61 CYS cc_start: 0.8655 (t) cc_final: 0.8145 (m) REVERT: D 102 TRP cc_start: 0.8281 (t-100) cc_final: 0.8040 (t-100) REVERT: C 83 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: C 118 TYR cc_start: 0.7364 (t80) cc_final: 0.7049 (t80) REVERT: h 7 SER cc_start: 0.6692 (m) cc_final: 0.6359 (t) REVERT: h 13 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7121 (tm-30) REVERT: h 64 VAL cc_start: 0.7250 (m) cc_final: 0.6966 (p) REVERT: h 95 PHE cc_start: 0.6361 (m-80) cc_final: 0.6147 (m-80) REVERT: l 29 LEU cc_start: 0.8261 (mt) cc_final: 0.7811 (mt) REVERT: l 31 HIS cc_start: 0.6871 (t-90) cc_final: 0.6328 (t-90) REVERT: l 33 ASN cc_start: 0.8279 (t0) cc_final: 0.8016 (t0) REVERT: L 84 GLU cc_start: 0.7137 (pm20) cc_final: 0.6063 (pm20) outliers start: 42 outliers final: 29 residues processed: 282 average time/residue: 0.1791 time to fit residues: 69.2387 Evaluate side-chains 287 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 16 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 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 h residue 84 ASN Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 95 optimal weight: 0.0170 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS H 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.140543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120338 restraints weight = 17531.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.123967 restraints weight = 10310.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.126416 restraints weight = 6925.921| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8261 Z= 0.183 Angle : 0.693 9.467 11259 Z= 0.352 Chirality : 0.045 0.398 1230 Planarity : 0.005 0.061 1443 Dihedral : 4.732 50.794 1118 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 6.25 % Allowed : 27.50 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1001 helix: 1.40 (0.27), residues: 364 sheet: -0.19 (0.35), residues: 210 loop : -0.33 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 40 HIS 0.007 0.002 HIS A 51 PHE 0.026 0.002 PHE D 24 TYR 0.047 0.002 TYR A 88 ARG 0.006 0.001 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.04969 ( 385) hydrogen bonds : angle 5.12232 ( 1068) SS BOND : bond 0.00671 ( 4) SS BOND : angle 0.92722 ( 8) covalent geometry : bond 0.00389 ( 8257) covalent geometry : angle 0.69321 (11251) *********************** 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 342 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 0.807 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: 0.8309 (mp0) cc_final: 0.8056 (mp0) REVERT: B 57 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8045 (mm-40) REVERT: B 62 TRP cc_start: 0.8180 (t-100) cc_final: 0.7876 (t-100) REVERT: B 93 MET cc_start: 0.7874 (mtp) cc_final: 0.7461 (mtm) REVERT: A 39 ARG cc_start: 0.7637 (ttp-110) cc_final: 0.7357 (ttp-110) REVERT: A 55 LEU cc_start: 0.8669 (tp) cc_final: 0.8299 (tt) REVERT: D 61 CYS cc_start: 0.8657 (t) cc_final: 0.8217 (m) REVERT: D 102 TRP cc_start: 0.8449 (t-100) cc_final: 0.7956 (t-100) REVERT: C 64 GLU cc_start: 0.7181 (tt0) cc_final: 0.6845 (mt-10) REVERT: C 72 VAL cc_start: 0.9079 (t) cc_final: 0.8854 (p) REVERT: C 87 SER cc_start: 0.7605 (OUTLIER) cc_final: 0.7288 (t) REVERT: h 13 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7134 (tm-30) REVERT: h 64 VAL cc_start: 0.7208 (m) cc_final: 0.6963 (p) REVERT: h 95 PHE cc_start: 0.6331 (m-80) cc_final: 0.6060 (m-80) REVERT: l 31 HIS cc_start: 0.6856 (t-90) cc_final: 0.6421 (t-90) REVERT: l 33 ASN cc_start: 0.8377 (t0) cc_final: 0.8175 (t0) REVERT: l 38 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7156 (m-10) REVERT: H 18 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7818 (mt) REVERT: H 59 ASP cc_start: 0.7912 (t0) cc_final: 0.7663 (t0) REVERT: L 59 ARG cc_start: 0.8269 (mtt180) cc_final: 0.8019 (mtp180) outliers start: 55 outliers final: 37 residues processed: 307 average time/residue: 0.1789 time to fit residues: 75.2839 Evaluate side-chains 314 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 ILE 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 122 PHE Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN 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 107 CYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 67 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 87 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 0.0370 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.142395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.121873 restraints weight = 17615.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.125535 restraints weight = 10370.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.128026 restraints weight = 6982.309| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8261 Z= 0.118 Angle : 0.652 10.446 11259 Z= 0.323 Chirality : 0.042 0.197 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.536 50.691 1118 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 4.89 % Allowed : 30.11 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.27), residues: 1001 helix: 1.22 (0.26), residues: 372 sheet: -0.06 (0.36), residues: 210 loop : -0.31 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.005 0.001 HIS h 35 PHE 0.024 0.002 PHE C 23 TYR 0.050 0.002 TYR A 88 ARG 0.005 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 385) hydrogen bonds : angle 4.90591 ( 1068) SS BOND : bond 0.00464 ( 4) SS BOND : angle 1.04180 ( 8) covalent geometry : bond 0.00250 ( 8257) covalent geometry : angle 0.65120 (11251) *********************** 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 323 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 0.867 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: 0.8208 (mp0) cc_final: 0.7993 (mp0) REVERT: B 57 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7884 (mm-40) REVERT: B 62 TRP cc_start: 0.8187 (t-100) cc_final: 0.7843 (t-100) REVERT: B 93 MET cc_start: 0.7757 (mtp) cc_final: 0.7276 (mtm) REVERT: A 8 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7096 (tp30) REVERT: A 23 PHE cc_start: 0.3934 (OUTLIER) cc_final: 0.2943 (m-80) REVERT: A 65 LEU cc_start: 0.8214 (mm) cc_final: 0.8004 (mp) REVERT: A 127 ARG cc_start: 0.3633 (OUTLIER) cc_final: 0.2162 (tmt170) REVERT: D 60 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8078 (mm) REVERT: D 61 CYS cc_start: 0.8652 (t) cc_final: 0.8169 (m) REVERT: D 97 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7813 (tt) REVERT: C 64 GLU cc_start: 0.7199 (tt0) cc_final: 0.6903 (mt-10) REVERT: C 72 VAL cc_start: 0.9033 (t) cc_final: 0.8792 (p) REVERT: h 13 GLN cc_start: 0.7623 (tm-30) cc_final: 0.6980 (tm-30) REVERT: h 64 VAL cc_start: 0.7194 (m) cc_final: 0.6944 (p) REVERT: h 95 PHE cc_start: 0.6300 (m-80) cc_final: 0.6084 (m-80) REVERT: l 31 HIS cc_start: 0.6904 (t-90) cc_final: 0.6377 (t-90) REVERT: l 33 ASN cc_start: 0.8460 (t0) cc_final: 0.8230 (t0) REVERT: l 38 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7249 (m-10) REVERT: H 18 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7662 (mt) REVERT: H 59 ASP cc_start: 0.7887 (t0) cc_final: 0.7639 (t0) REVERT: L 24 ARG cc_start: 0.5801 (tpp-160) cc_final: 0.5566 (tpp-160) REVERT: L 84 GLU cc_start: 0.7471 (pm20) cc_final: 0.6254 (pm20) REVERT: L 108 LYS cc_start: 0.7550 (tppt) cc_final: 0.7301 (tppt) outliers start: 43 outliers final: 29 residues processed: 300 average time/residue: 0.1800 time to fit residues: 73.7152 Evaluate side-chains 306 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 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 60 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 107 CYS Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 57 ASN Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain 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 90 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 68 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 GLN ** 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 = 0.4016 r_free = 0.4016 target = 0.143065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.122822 restraints weight = 17604.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.126460 restraints weight = 10297.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128956 restraints weight = 6879.826| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8261 Z= 0.137 Angle : 0.672 9.592 11259 Z= 0.332 Chirality : 0.043 0.236 1230 Planarity : 0.005 0.061 1443 Dihedral : 4.545 52.246 1118 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 1001 helix: 1.27 (0.27), residues: 372 sheet: -0.10 (0.36), residues: 210 loop : -0.31 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 47 HIS 0.010 0.001 HIS h 35 PHE 0.023 0.002 PHE C 23 TYR 0.051 0.002 TYR A 88 ARG 0.004 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 385) hydrogen bonds : angle 4.89116 ( 1068) SS BOND : bond 0.00648 ( 4) SS BOND : angle 1.11663 ( 8) covalent geometry : bond 0.00296 ( 8257) covalent geometry : angle 0.67167 (11251) *********************** 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 320 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 0.836 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: 0.8308 (mp0) cc_final: 0.8083 (mp0) REVERT: B 57 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7921 (mm-40) REVERT: B 62 TRP cc_start: 0.8228 (t-100) cc_final: 0.7920 (t-100) REVERT: B 93 MET cc_start: 0.7751 (mtp) cc_final: 0.7374 (mtm) REVERT: A 23 PHE cc_start: 0.4056 (OUTLIER) cc_final: 0.2960 (m-80) REVERT: A 93 MET cc_start: 0.7991 (ttm) cc_final: 0.7749 (ttm) REVERT: A 105 ILE cc_start: 0.8875 (tp) cc_final: 0.8505 (tp) REVERT: A 127 ARG cc_start: 0.3686 (OUTLIER) cc_final: 0.2216 (tmt170) REVERT: D 61 CYS cc_start: 0.8636 (t) cc_final: 0.8109 (m) REVERT: D 97 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7877 (tt) REVERT: D 102 TRP cc_start: 0.8348 (t-100) cc_final: 0.8043 (t60) REVERT: C 64 GLU cc_start: 0.7272 (tt0) cc_final: 0.6897 (mt-10) REVERT: C 72 VAL cc_start: 0.9079 (t) cc_final: 0.8860 (p) REVERT: C 118 TYR cc_start: 0.7730 (t80) cc_final: 0.7154 (t80) REVERT: h 13 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7022 (tm-30) REVERT: h 64 VAL cc_start: 0.7139 (m) cc_final: 0.6898 (p) REVERT: h 95 PHE cc_start: 0.6289 (m-80) cc_final: 0.6076 (m-80) REVERT: l 31 HIS cc_start: 0.6916 (t-90) cc_final: 0.6433 (t-90) REVERT: l 33 ASN cc_start: 0.8479 (t0) cc_final: 0.8275 (t0) REVERT: l 38 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.7202 (m-10) REVERT: H 59 ASP cc_start: 0.7943 (t0) cc_final: 0.7688 (t0) REVERT: L 24 ARG cc_start: 0.6043 (tpp-160) cc_final: 0.5795 (tpp-160) REVERT: L 84 GLU cc_start: 0.7457 (pm20) cc_final: 0.6262 (pm20) outliers start: 43 outliers final: 32 residues processed: 297 average time/residue: 0.1751 time to fit residues: 71.6857 Evaluate side-chains 307 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 23 PHE Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 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 5 THR Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain l residue 77 THR Chi-restraints excluded: chain H residue 40 VAL 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 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 45 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.2980 chunk 63 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 GLN ** 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 = 0.4021 r_free = 0.4021 target = 0.143184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122937 restraints weight = 18058.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.126760 restraints weight = 10346.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.129282 restraints weight = 6798.086| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8261 Z= 0.116 Angle : 0.664 11.074 11259 Z= 0.322 Chirality : 0.042 0.197 1230 Planarity : 0.005 0.060 1443 Dihedral : 4.455 52.832 1118 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 3.75 % Allowed : 32.16 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.27), residues: 1001 helix: 1.12 (0.27), residues: 372 sheet: -0.06 (0.36), residues: 210 loop : -0.27 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 HIS 0.007 0.001 HIS h 35 PHE 0.025 0.002 PHE C 23 TYR 0.054 0.001 TYR A 88 ARG 0.005 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 385) hydrogen bonds : angle 4.80170 ( 1068) SS BOND : bond 0.00636 ( 4) SS BOND : angle 0.97252 ( 8) covalent geometry : bond 0.00248 ( 8257) covalent geometry : angle 0.66330 (11251) *********************** 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 308 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.817 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: 0.8358 (mp0) cc_final: 0.8101 (mp0) REVERT: B 57 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7915 (mm-40) REVERT: B 93 MET cc_start: 0.7785 (mtp) cc_final: 0.7532 (mtp) REVERT: B 99 GLN cc_start: 0.8661 (mt0) cc_final: 0.8122 (tt0) REVERT: A 23 PHE cc_start: 0.4039 (OUTLIER) cc_final: 0.3030 (m-80) REVERT: A 93 MET cc_start: 0.8055 (ttm) cc_final: 0.7783 (ttm) REVERT: A 105 ILE cc_start: 0.8879 (tp) cc_final: 0.8532 (tp) REVERT: A 127 ARG cc_start: 0.3615 (OUTLIER) cc_final: 0.2096 (tmt170) REVERT: D 60 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8071 (mm) REVERT: D 61 CYS cc_start: 0.8599 (t) cc_final: 0.8066 (m) REVERT: C 64 GLU cc_start: 0.7318 (tt0) cc_final: 0.6937 (mt-10) REVERT: C 72 VAL cc_start: 0.9037 (t) cc_final: 0.8820 (p) REVERT: C 93 MET cc_start: 0.7944 (ttm) cc_final: 0.7663 (ptp) REVERT: C 118 TYR cc_start: 0.7671 (t80) cc_final: 0.7162 (t80) REVERT: h 7 SER cc_start: 0.7077 (t) cc_final: 0.6835 (t) REVERT: h 13 GLN cc_start: 0.7601 (tm-30) cc_final: 0.6915 (tm-30) REVERT: h 64 VAL cc_start: 0.7150 (m) cc_final: 0.6908 (p) REVERT: l 38 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7209 (m-10) REVERT: H 59 ASP cc_start: 0.7986 (t0) cc_final: 0.7704 (t0) REVERT: L 24 ARG cc_start: 0.6030 (tpp-160) cc_final: 0.5822 (tpp-160) REVERT: L 84 GLU cc_start: 0.7477 (pm20) cc_final: 0.6256 (pm20) outliers start: 33 outliers final: 26 residues processed: 290 average time/residue: 0.1873 time to fit residues: 74.0132 Evaluate side-chains 301 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 23 PHE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain D residue 33 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 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 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 5 THR 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 7 SER 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 90 optimal weight: 0.0040 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS L 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.134817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.114626 restraints weight = 18189.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.118270 restraints weight = 10534.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.120739 restraints weight = 7000.401| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8261 Z= 0.218 Angle : 0.755 13.117 11259 Z= 0.390 Chirality : 0.047 0.192 1230 Planarity : 0.006 0.062 1443 Dihedral : 5.125 59.120 1118 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.09 % Favored : 94.81 % Rotamer: Outliers : 4.43 % Allowed : 31.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 1001 helix: 0.90 (0.27), residues: 371 sheet: -0.09 (0.38), residues: 194 loop : -0.44 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP H 47 HIS 0.006 0.002 HIS B 51 PHE 0.037 0.003 PHE H 68 TYR 0.061 0.002 TYR A 88 ARG 0.007 0.001 ARG B 112 Details of bonding type rmsd hydrogen bonds : bond 0.05683 ( 385) hydrogen bonds : angle 5.23912 ( 1068) SS BOND : bond 0.01023 ( 4) SS BOND : angle 1.61052 ( 8) covalent geometry : bond 0.00458 ( 8257) covalent geometry : angle 0.75445 (11251) *********************** 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 335 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8566 (mp0) cc_final: 0.8159 (mp0) REVERT: B 57 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8078 (mm-40) REVERT: B 67 ASN cc_start: 0.8252 (m-40) cc_final: 0.7990 (m-40) REVERT: B 127 ARG cc_start: 0.3291 (tpt170) cc_final: 0.2777 (tmt170) REVERT: A 8 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7304 (tp30) REVERT: A 23 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.3589 (m-80) REVERT: A 53 THR cc_start: 0.7903 (p) cc_final: 0.7436 (t) REVERT: A 93 MET cc_start: 0.8066 (ttm) cc_final: 0.7822 (ttm) REVERT: A 105 ILE cc_start: 0.9027 (tp) cc_final: 0.8678 (tp) REVERT: D 61 CYS cc_start: 0.8638 (t) cc_final: 0.8161 (m) REVERT: D 102 TRP cc_start: 0.8921 (t60) cc_final: 0.7815 (t60) REVERT: C 60 LEU cc_start: 0.8517 (mt) cc_final: 0.8161 (mt) REVERT: C 64 GLU cc_start: 0.7322 (tt0) cc_final: 0.6918 (mt-10) REVERT: C 87 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7529 (t) REVERT: h 48 LEU cc_start: 0.8425 (mt) cc_final: 0.8208 (mt) REVERT: l 27 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7864 (tm-30) REVERT: l 38 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7166 (m-10) REVERT: l 72 SER cc_start: 0.7900 (t) cc_final: 0.7687 (m) REVERT: H 59 ASP cc_start: 0.8060 (t0) cc_final: 0.7771 (t0) REVERT: L 52 LEU cc_start: 0.7582 (mt) cc_final: 0.7287 (mt) outliers start: 39 outliers final: 29 residues processed: 316 average time/residue: 0.1781 time to fit residues: 77.1821 Evaluate side-chains 327 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 27 ILE Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 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 87 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain h residue 108 SER Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain H residue 4 LEU 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 90 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.115705 restraints weight = 17465.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.119311 restraints weight = 10185.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.121701 restraints weight = 6821.768| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8261 Z= 0.217 Angle : 0.800 15.458 11259 Z= 0.406 Chirality : 0.050 0.394 1230 Planarity : 0.006 0.062 1443 Dihedral : 5.195 58.739 1118 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 4.32 % Allowed : 32.16 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 1001 helix: 0.81 (0.26), residues: 371 sheet: -0.25 (0.37), residues: 194 loop : -0.65 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP H 47 HIS 0.007 0.001 HIS C 104 PHE 0.060 0.003 PHE H 68 TYR 0.062 0.002 TYR A 88 ARG 0.007 0.001 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.05502 ( 385) hydrogen bonds : angle 5.32716 ( 1068) SS BOND : bond 0.00991 ( 4) SS BOND : angle 1.68171 ( 8) covalent geometry : bond 0.00461 ( 8257) covalent geometry : angle 0.79875 (11251) ********************** 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 338 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7837 (ttpp) REVERT: B 14 GLU cc_start: 0.8561 (mp0) cc_final: 0.8137 (mp0) REVERT: B 57 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8056 (mm-40) REVERT: B 67 ASN cc_start: 0.8217 (m-40) cc_final: 0.7946 (m-40) REVERT: B 99 GLN cc_start: 0.8630 (mt0) cc_final: 0.8252 (tt0) REVERT: B 127 ARG cc_start: 0.3294 (tpt170) cc_final: 0.2775 (tmt170) REVERT: A 8 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: A 23 PHE cc_start: 0.4427 (OUTLIER) cc_final: 0.3539 (m-80) REVERT: A 93 MET cc_start: 0.8087 (ttm) cc_final: 0.7788 (ttm) REVERT: A 105 ILE cc_start: 0.9008 (tp) cc_final: 0.8619 (tp) REVERT: D 30 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8345 (tt) REVERT: D 60 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8192 (mm) REVERT: D 61 CYS cc_start: 0.8627 (t) cc_final: 0.8171 (m) REVERT: D 92 ASN cc_start: 0.8893 (m-40) cc_final: 0.8692 (m-40) REVERT: D 102 TRP cc_start: 0.8850 (t60) cc_final: 0.7682 (t60) REVERT: C 60 LEU cc_start: 0.8487 (mt) cc_final: 0.8159 (mt) REVERT: C 64 GLU cc_start: 0.7354 (tt0) cc_final: 0.6976 (mt-10) REVERT: C 87 SER cc_start: 0.7956 (m) cc_final: 0.7556 (t) REVERT: h 13 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7030 (tm-30) REVERT: l 27 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7864 (tm-30) REVERT: l 33 ASN cc_start: 0.8642 (t0) cc_final: 0.8279 (p0) REVERT: l 38 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7074 (m-10) REVERT: H 59 ASP cc_start: 0.8087 (t0) cc_final: 0.7763 (t0) REVERT: L 52 LEU cc_start: 0.7542 (mt) cc_final: 0.7312 (mt) REVERT: L 84 GLU cc_start: 0.7516 (pm20) cc_final: 0.6158 (pm20) outliers start: 38 outliers final: 30 residues processed: 317 average time/residue: 0.1744 time to fit residues: 75.9364 Evaluate side-chains 330 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 295 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 51 HIS Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 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 121 SER Chi-restraints excluded: chain h residue 40 VAL Chi-restraints excluded: chain l residue 9 LEU Chi-restraints excluded: chain l residue 38 PHE Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 67 PHE Chi-restraints excluded: chain H residue 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 90 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 81 optimal weight: 0.0020 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 HIS h 111 GLN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.136486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116334 restraints weight = 17529.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.119905 restraints weight = 10279.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.122347 restraints weight = 6890.776| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8261 Z= 0.162 Angle : 0.776 14.485 11259 Z= 0.387 Chirality : 0.047 0.303 1230 Planarity : 0.005 0.060 1443 Dihedral : 5.062 58.075 1118 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.09 % Favored : 94.81 % Rotamer: Outliers : 3.98 % Allowed : 33.07 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 1001 helix: 0.91 (0.27), residues: 369 sheet: -0.10 (0.38), residues: 184 loop : -0.72 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP H 47 HIS 0.005 0.001 HIS B 51 PHE 0.049 0.002 PHE H 68 TYR 0.062 0.002 TYR A 88 ARG 0.006 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 385) hydrogen bonds : angle 5.17804 ( 1068) SS BOND : bond 0.00954 ( 4) SS BOND : angle 1.57710 ( 8) covalent geometry : bond 0.00348 ( 8257) covalent geometry : angle 0.77498 (11251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.59 seconds wall clock time: 53 minutes 8.91 seconds (3188.91 seconds total)