Starting phenix.real_space_refine on Sat Jul 4 05:28:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h9m_51969/07_2026/9h9m_51969_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h9m_51969/07_2026/9h9m_51969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h9m_51969/07_2026/9h9m_51969_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h9m_51969/07_2026/9h9m_51969_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h9m_51969/07_2026/9h9m_51969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h9m_51969/07_2026/9h9m_51969.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 42 5.21 5 S 27 5.16 5 C 9805 2.51 5 N 3435 2.21 5 O 4719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18485 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 36, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 169} Link IDs: {'rna2p': 72, 'rna3p': 383} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1095 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "I" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 803 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "1" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Unusual residues: {' MG': 41} Classifications: {'undetermined': 41} Link IDs: {None: 40} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.76, per 1000 atoms: 0.20 Number of scatterers: 18485 At special positions: 0 Unit cell: (140.238, 117.978, 168.063, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 456 15.00 Mg 42 11.99 O 4719 8.00 N 3435 7.00 C 9805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.73 Conformation dependent library (CDL) restraints added in 460.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2036 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 51.7% alpha, 15.5% beta 131 base pairs and 220 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.635A pdb=" N MET B 27 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 63 removed outlier: 3.507A pdb=" N THR B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 75 through 87 removed outlier: 4.522A pdb=" N ALA B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.670A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 206 through 226 Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.669A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 48 removed outlier: 4.841A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 63 removed outlier: 4.382A pdb=" N LYS C 62 " --> pdb=" O ARG C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 removed outlier: 4.405A pdb=" N VAL C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 82 Processing helix chain 'C' and resid 83 through 96 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 146 Processing helix chain 'C' and resid 157 through 160 Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.505A pdb=" N ALA G 24 " --> pdb=" O SER G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.516A pdb=" N LYS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 133 through 141 removed outlier: 3.709A pdb=" N VAL G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 4.380A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET I 46 " --> pdb=" O GLU I 42 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 101 Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.629A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.924A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 3.710A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 84 removed outlier: 3.569A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.612A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.733A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix Processing helix chain 'N' and resid 81 through 91 removed outlier: 3.536A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.834A pdb=" N PHE B 90 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU B 68 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 161 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE B 186 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL B 163 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 183 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 200 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA B 185 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.854A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 164 through 170 Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 74 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.420A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 36 through 52 removed outlier: 3.862A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU J 73 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU J 71 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR J 69 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG J 45 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE J 67 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU J 47 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR J 65 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE J 49 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP J 63 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 36 through 52 removed outlier: 3.862A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU J 73 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU J 71 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR J 69 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG J 45 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE J 67 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU J 47 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR J 65 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE J 49 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP J 63 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 73 through 74 removed outlier: 3.837A pdb=" N LEU N 79 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.078A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 333 hydrogen bonds 548 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 220 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2683 1.33 - 1.45: 7554 1.45 - 1.57: 8533 1.57 - 1.70: 912 1.70 - 1.82: 51 Bond restraints: 19733 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.468 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.465 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CA GLN B 19 " pdb=" C GLN B 19 " ideal model delta sigma weight residual 1.527 1.477 0.050 1.35e-02 5.49e+03 1.35e+01 bond pdb=" CA ALA M 18 " pdb=" CB ALA M 18 " ideal model delta sigma weight residual 1.530 1.475 0.055 1.57e-02 4.06e+03 1.22e+01 bond pdb=" CA PHE B 32 " pdb=" C PHE B 32 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.24e-02 6.50e+03 1.19e+01 ... (remaining 19728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 28606 3.01 - 6.01: 208 6.01 - 9.02: 31 9.02 - 12.03: 12 12.03 - 15.03: 2 Bond angle restraints: 28859 Sorted by residual: angle pdb=" N VAL J 57 " pdb=" CA VAL J 57 " pdb=" C VAL J 57 " ideal model delta sigma weight residual 109.58 123.25 -13.67 1.29e+00 6.01e-01 1.12e+02 angle pdb=" N ASN J 58 " pdb=" CA ASN J 58 " pdb=" C ASN J 58 " ideal model delta sigma weight residual 108.90 93.87 15.03 1.63e+00 3.76e-01 8.51e+01 angle pdb=" N TRP B 23 " pdb=" CA TRP B 23 " pdb=" C TRP B 23 " ideal model delta sigma weight residual 111.74 122.56 -10.82 1.35e+00 5.49e-01 6.42e+01 angle pdb=" N HIS J 56 " pdb=" CA HIS J 56 " pdb=" C HIS J 56 " ideal model delta sigma weight residual 109.07 97.69 11.38 1.61e+00 3.86e-01 4.99e+01 angle pdb=" N ILE M 17 " pdb=" CA ILE M 17 " pdb=" C ILE M 17 " ideal model delta sigma weight residual 110.62 103.47 7.15 1.02e+00 9.61e-01 4.92e+01 ... (remaining 28854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 11477 35.38 - 70.75: 988 70.75 - 106.13: 138 106.13 - 141.51: 4 141.51 - 176.89: 2 Dihedral angle restraints: 12609 sinusoidal: 9463 harmonic: 3146 Sorted by residual: dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual -128.00 48.89 -176.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 11381 " pdb=" C1' U 11381 " pdb=" N1 U 11381 " pdb=" C2 U 11381 " ideal model delta sinusoidal sigma weight residual -160.00 -45.80 -114.20 1 1.50e+01 4.44e-03 6.02e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 94.17 105.83 1 1.50e+01 4.44e-03 5.43e+01 ... (remaining 12606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3477 0.100 - 0.199: 116 0.199 - 0.299: 7 0.299 - 0.399: 1 0.399 - 0.498: 1 Chirality restraints: 3602 Sorted by residual: chirality pdb=" P C 1 931 " pdb=" OP1 C 1 931 " pdb=" OP2 C 1 931 " pdb=" O5' C 1 931 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA TRP B 23 " pdb=" N TRP B 23 " pdb=" C TRP B 23 " pdb=" CB TRP B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ILE B 200 " pdb=" N ILE B 200 " pdb=" C ILE B 200 " pdb=" CB ILE B 200 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3599 not shown) Planarity restraints: 1982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " 0.020 2.00e-02 2.50e+03 2.20e-02 1.58e+01 pdb=" N9 2MG 11207 " -0.007 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " -0.010 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " -0.014 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " -0.002 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " -0.000 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " -0.012 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " 0.011 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " 0.019 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " 0.032 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " 0.017 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " 0.006 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " -0.009 2.00e-02 2.50e+03 1.40e-02 6.39e+00 pdb=" N9 2MG 1 966 " 0.002 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " 0.007 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " 0.009 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " 0.002 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " 0.002 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " 0.007 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " -0.006 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " -0.013 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " -0.021 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " -0.013 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " -0.004 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 16 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C PHE B 16 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE B 16 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY B 17 " -0.014 2.00e-02 2.50e+03 ... (remaining 1979 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 179 2.52 - 3.12: 14187 3.12 - 3.71: 34036 3.71 - 4.31: 48060 4.31 - 4.90: 68141 Nonbonded interactions: 164603 Sorted by model distance: nonbonded pdb=" OD2 ASP B 205 " pdb="ZN ZN B 301 " model vdw 1.930 2.230 nonbonded pdb=" OD2 ASP B 188 " pdb="ZN ZN B 301 " model vdw 2.005 2.230 nonbonded pdb=" OD1 ASP B 204 " pdb="ZN ZN B 301 " model vdw 2.052 2.230 nonbonded pdb=" OG SER M 46 " pdb=" OE2 GLU M 47 " model vdw 2.067 3.040 nonbonded pdb=" O2' U 11183 " pdb=" OP1 G 11184 " model vdw 2.068 3.040 ... (remaining 164598 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 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: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 22.110 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 19734 Z= 0.289 Angle : 0.712 15.035 28859 Z= 0.459 Chirality : 0.041 0.498 3602 Planarity : 0.005 0.078 1982 Dihedral : 21.291 176.886 10573 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1084 helix: -0.07 (0.22), residues: 502 sheet: 0.48 (0.43), residues: 158 loop : -0.45 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 90 TYR 0.018 0.002 TYR N 20 PHE 0.016 0.002 PHE B 90 TRP 0.007 0.001 TRP S 34 HIS 0.005 0.001 HIS N 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.29 (19733) covalent geometry : angle 0.71192 / 0.46 (28859) hydrogen bonds : bond 0.17007 / 16.59 ( 758) hydrogen bonds : angle 6.20298 / 8.03 ( 1748) metal coordination : bond 0.09449 / 4.72 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 11 ASP cc_start: 0.6516 (p0) cc_final: 0.6221 (p0) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1553 time to fit residues: 40.3121 Evaluate side-chains 128 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 0.2980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 ASN G 68 ASN I 50 GLN I 126 GLN J 56 HIS J 64 GLN M 8 ASN N 43 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.047226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.035377 restraints weight = 129633.409| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.01 r_work: 0.2904 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19734 Z= 0.141 Angle : 0.585 9.052 28859 Z= 0.335 Chirality : 0.039 0.316 3602 Planarity : 0.004 0.029 1982 Dihedral : 21.930 179.735 8364 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.42 % Allowed : 13.54 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.25), residues: 1084 helix: 0.92 (0.23), residues: 509 sheet: 0.62 (0.40), residues: 170 loop : -0.03 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 109 TYR 0.016 0.002 TYR I 38 PHE 0.022 0.002 PHE B 90 TRP 0.016 0.002 TRP B 23 HIS 0.010 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (19733) covalent geometry : angle 0.58480 / 0.33 (28859) hydrogen bonds : bond 0.07033 / 6.76 ( 758) hydrogen bonds : angle 4.34853 / 5.48 ( 1748) metal coordination : bond 0.00934 / 0.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9214 (tpp) cc_final: 0.8989 (tpp) REVERT: C 152 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7829 (tm-30) REVERT: C 165 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8796 (t) REVERT: J 30 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8854 (mmmt) REVERT: J 47 GLU cc_start: 0.8142 (mp0) cc_final: 0.7901 (mp0) REVERT: J 63 ASP cc_start: 0.8226 (t0) cc_final: 0.8008 (t0) REVERT: J 68 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8683 (mtt180) REVERT: J 97 ASP cc_start: 0.8080 (t0) cc_final: 0.7863 (t0) REVERT: M 42 ASP cc_start: 0.8545 (p0) cc_final: 0.8114 (p0) REVERT: N 10 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8244 (tt0) outliers start: 13 outliers final: 7 residues processed: 164 average time/residue: 0.1415 time to fit residues: 34.4696 Evaluate side-chains 141 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 10 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 119 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 130 ASN I 110 GLN M 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.044777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.032831 restraints weight = 132842.781| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.92 r_work: 0.2792 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19734 Z= 0.313 Angle : 0.670 8.867 28859 Z= 0.385 Chirality : 0.045 0.337 3602 Planarity : 0.005 0.046 1982 Dihedral : 21.818 178.423 8364 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.84 % Allowed : 14.85 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.25), residues: 1084 helix: 0.80 (0.23), residues: 501 sheet: 0.41 (0.40), residues: 162 loop : -0.38 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 49 TYR 0.025 0.002 TYR C 168 PHE 0.020 0.002 PHE B 90 TRP 0.014 0.002 TRP G 103 HIS 0.009 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.31 (19733) covalent geometry : angle 0.67006 / 0.38 (28859) hydrogen bonds : bond 0.08889 / 8.88 ( 758) hydrogen bonds : angle 4.44225 / 5.53 ( 1748) metal coordination : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9270 (tpp) cc_final: 0.8963 (tpp) REVERT: C 152 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7781 (tm-30) REVERT: G 136 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8416 (mmtt) REVERT: I 126 GLN cc_start: 0.8830 (mt0) cc_final: 0.8604 (tt0) REVERT: J 30 LYS cc_start: 0.9325 (mmmt) cc_final: 0.8968 (mmmt) REVERT: J 97 ASP cc_start: 0.8308 (t0) cc_final: 0.8094 (t0) REVERT: J 99 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7912 (tm-30) REVERT: N 10 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: N 39 GLU cc_start: 0.9035 (tp30) cc_final: 0.8788 (tp30) REVERT: N 54 ASP cc_start: 0.9008 (m-30) cc_final: 0.8699 (t0) outliers start: 26 outliers final: 15 residues processed: 146 average time/residue: 0.1354 time to fit residues: 29.9074 Evaluate side-chains 138 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain N residue 10 GLU Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS I 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.045821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.033979 restraints weight = 131100.471| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.85 r_work: 0.2840 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19734 Z= 0.136 Angle : 0.541 9.544 28859 Z= 0.315 Chirality : 0.038 0.305 3602 Planarity : 0.004 0.065 1982 Dihedral : 21.841 178.940 8364 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.97 % Allowed : 15.17 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1084 helix: 1.08 (0.23), residues: 501 sheet: 0.66 (0.41), residues: 162 loop : -0.31 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 90 TYR 0.015 0.002 TYR C 168 PHE 0.020 0.001 PHE B 90 TRP 0.034 0.002 TRP B 104 HIS 0.016 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (19733) covalent geometry : angle 0.54076 / 0.32 (28859) hydrogen bonds : bond 0.06050 / 5.66 ( 758) hydrogen bonds : angle 4.02195 / 5.04 ( 1748) metal coordination : bond 0.00306 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9296 (tpp) cc_final: 0.8945 (tpp) REVERT: G 136 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8383 (mmtm) REVERT: J 63 ASP cc_start: 0.8714 (t0) cc_final: 0.8205 (t0) REVERT: J 97 ASP cc_start: 0.8280 (t0) cc_final: 0.7985 (t0) REVERT: J 99 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7941 (tm-30) REVERT: N 39 GLU cc_start: 0.8971 (tp30) cc_final: 0.8737 (tp30) REVERT: N 89 MET cc_start: 0.8896 (mmm) cc_final: 0.8680 (mmm) outliers start: 18 outliers final: 12 residues processed: 148 average time/residue: 0.1374 time to fit residues: 30.6462 Evaluate side-chains 135 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain S residue 12 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 117 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS G 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.044930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.033285 restraints weight = 131609.147| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.79 r_work: 0.2796 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19734 Z= 0.224 Angle : 0.585 11.007 28859 Z= 0.334 Chirality : 0.040 0.382 3602 Planarity : 0.005 0.057 1982 Dihedral : 21.781 178.441 8364 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.95 % Allowed : 14.96 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1084 helix: 1.09 (0.23), residues: 496 sheet: 0.42 (0.40), residues: 162 loop : -0.32 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 45 TYR 0.017 0.002 TYR C 168 PHE 0.014 0.002 PHE B 90 TRP 0.038 0.002 TRP B 104 HIS 0.011 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 (19733) covalent geometry : angle 0.58485 / 0.33 (28859) hydrogen bonds : bond 0.07029 / 6.90 ( 758) hydrogen bonds : angle 4.09963 / 5.11 ( 1748) metal coordination : bond 0.00165 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9346 (tpp) cc_final: 0.8978 (tpp) REVERT: B 168 HIS cc_start: 0.8807 (t70) cc_final: 0.8572 (t-170) REVERT: G 136 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8488 (mmtm) REVERT: J 97 ASP cc_start: 0.8369 (t0) cc_final: 0.8086 (t0) REVERT: J 99 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8087 (tm-30) REVERT: N 54 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8718 (t70) REVERT: N 89 MET cc_start: 0.8933 (mmm) cc_final: 0.8715 (mmm) outliers start: 27 outliers final: 13 residues processed: 140 average time/residue: 0.1358 time to fit residues: 28.7304 Evaluate side-chains 133 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain N residue 54 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 124 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.045597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.033762 restraints weight = 127943.917| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 3.88 r_work: 0.2831 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19734 Z= 0.123 Angle : 0.526 9.486 28859 Z= 0.304 Chirality : 0.038 0.295 3602 Planarity : 0.004 0.034 1982 Dihedral : 21.786 178.870 8364 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.40 % Allowed : 15.61 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1084 helix: 1.24 (0.24), residues: 494 sheet: 0.61 (0.40), residues: 161 loop : -0.24 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 132 TYR 0.013 0.002 TYR C 168 PHE 0.028 0.001 PHE I 127 TRP 0.032 0.002 TRP B 104 HIS 0.004 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (19733) covalent geometry : angle 0.52634 / 0.30 (28859) hydrogen bonds : bond 0.05668 / 5.28 ( 758) hydrogen bonds : angle 3.91160 / 4.90 ( 1748) metal coordination : bond 0.00210 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9359 (tpp) cc_final: 0.8970 (tpp) REVERT: B 168 HIS cc_start: 0.8818 (t70) cc_final: 0.8612 (t-170) REVERT: G 103 TRP cc_start: 0.9136 (m-10) cc_final: 0.8651 (m-10) REVERT: G 136 LYS cc_start: 0.8777 (mmtm) cc_final: 0.8514 (mmtt) REVERT: I 124 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8090 (ptt90) REVERT: J 30 LYS cc_start: 0.9326 (mmmt) cc_final: 0.9055 (mmmt) REVERT: J 63 ASP cc_start: 0.8743 (t0) cc_final: 0.8442 (t0) REVERT: J 97 ASP cc_start: 0.8347 (t0) cc_final: 0.8039 (t0) REVERT: J 99 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8026 (tm-30) REVERT: N 39 GLU cc_start: 0.8915 (tp30) cc_final: 0.8692 (tp30) REVERT: N 54 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8659 (t70) outliers start: 22 outliers final: 13 residues processed: 148 average time/residue: 0.1429 time to fit residues: 31.7201 Evaluate side-chains 143 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 124 ARG Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain S residue 12 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 150 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.045080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.033441 restraints weight = 129440.444| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.80 r_work: 0.2805 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19734 Z= 0.191 Angle : 0.562 13.264 28859 Z= 0.320 Chirality : 0.039 0.274 3602 Planarity : 0.004 0.037 1982 Dihedral : 21.724 178.478 8364 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.40 % Allowed : 16.70 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.26), residues: 1084 helix: 1.13 (0.24), residues: 500 sheet: 0.56 (0.41), residues: 161 loop : -0.22 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 111 TYR 0.016 0.002 TYR C 168 PHE 0.011 0.001 PHE B 90 TRP 0.024 0.002 TRP B 104 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (19733) covalent geometry : angle 0.56161 / 0.32 (28859) hydrogen bonds : bond 0.06253 / 6.00 ( 758) hydrogen bonds : angle 4.00659 / 4.96 ( 1748) metal coordination : bond 0.00157 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.543 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 100 MET cc_start: 0.9367 (tpp) cc_final: 0.9018 (tpp) REVERT: B 147 SER cc_start: 0.8775 (t) cc_final: 0.8535 (p) REVERT: G 136 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8541 (mmtt) REVERT: I 124 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7993 (ptt90) REVERT: J 30 LYS cc_start: 0.9328 (mmmt) cc_final: 0.9044 (mmmt) REVERT: J 63 ASP cc_start: 0.8794 (t0) cc_final: 0.8332 (t0) REVERT: J 97 ASP cc_start: 0.8404 (t0) cc_final: 0.8096 (t0) REVERT: J 99 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8082 (tm-30) REVERT: M 28 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9148 (p) REVERT: N 39 GLU cc_start: 0.9022 (tp30) cc_final: 0.8788 (tp30) REVERT: N 54 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8693 (t70) outliers start: 22 outliers final: 14 residues processed: 139 average time/residue: 0.1375 time to fit residues: 29.2159 Evaluate side-chains 142 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 124 ARG Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 54 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 69 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 150 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.045917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.034239 restraints weight = 128344.092| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.75 r_work: 0.2853 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19734 Z= 0.114 Angle : 0.530 11.374 28859 Z= 0.301 Chirality : 0.036 0.313 3602 Planarity : 0.004 0.037 1982 Dihedral : 21.733 178.954 8364 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.40 % Allowed : 17.14 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1084 helix: 1.18 (0.24), residues: 499 sheet: 0.69 (0.41), residues: 161 loop : -0.07 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 119 TYR 0.015 0.002 TYR C 168 PHE 0.018 0.001 PHE I 127 TRP 0.024 0.001 TRP B 104 HIS 0.017 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (19733) covalent geometry : angle 0.52986 / 0.30 (28859) hydrogen bonds : bond 0.05258 / 4.84 ( 758) hydrogen bonds : angle 3.86156 / 4.85 ( 1748) metal coordination : bond 0.00174 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9357 (tpp) cc_final: 0.9020 (tpp) REVERT: B 147 SER cc_start: 0.8805 (t) cc_final: 0.8559 (p) REVERT: G 136 LYS cc_start: 0.8788 (mmtm) cc_final: 0.8505 (mmtt) REVERT: I 124 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8121 (ptt90) REVERT: J 30 LYS cc_start: 0.9292 (mmmt) cc_final: 0.9006 (mmmt) REVERT: J 63 ASP cc_start: 0.8729 (t0) cc_final: 0.8301 (t0) REVERT: J 97 ASP cc_start: 0.8362 (t0) cc_final: 0.8034 (t0) REVERT: J 99 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7976 (tm-30) REVERT: M 42 ASP cc_start: 0.9061 (p0) cc_final: 0.8723 (p0) REVERT: N 39 GLU cc_start: 0.8986 (tp30) cc_final: 0.8735 (tp30) REVERT: N 54 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8680 (t70) REVERT: S 29 LYS cc_start: 0.9039 (mmmt) cc_final: 0.8606 (mmmt) outliers start: 22 outliers final: 13 residues processed: 150 average time/residue: 0.1379 time to fit residues: 31.2511 Evaluate side-chains 150 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 124 ARG Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain N residue 54 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 43 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 0.0070 chunk 86 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN B 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.045605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.033906 restraints weight = 130307.048| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.86 r_work: 0.2836 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19734 Z= 0.144 Angle : 0.553 14.511 28859 Z= 0.309 Chirality : 0.038 0.411 3602 Planarity : 0.004 0.036 1982 Dihedral : 21.684 178.831 8364 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.18 % Allowed : 17.47 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1084 helix: 1.20 (0.24), residues: 499 sheet: 0.64 (0.40), residues: 163 loop : -0.09 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 111 TYR 0.017 0.002 TYR C 168 PHE 0.010 0.001 PHE S 74 TRP 0.019 0.001 TRP B 104 HIS 0.015 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (19733) covalent geometry : angle 0.55277 / 0.31 (28859) hydrogen bonds : bond 0.05602 / 5.25 ( 758) hydrogen bonds : angle 3.91197 / 4.92 ( 1748) metal coordination : bond 0.00115 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.358 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 100 MET cc_start: 0.9369 (tpp) cc_final: 0.9060 (tpp) REVERT: B 147 SER cc_start: 0.8820 (t) cc_final: 0.8550 (p) REVERT: B 168 HIS cc_start: 0.8808 (t70) cc_final: 0.8603 (t-170) REVERT: G 136 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8508 (mmtt) REVERT: I 124 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8069 (ptt90) REVERT: J 30 LYS cc_start: 0.9282 (mmmt) cc_final: 0.9002 (mmmt) REVERT: J 63 ASP cc_start: 0.8757 (t0) cc_final: 0.8316 (t0) REVERT: J 87 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9168 (pp) REVERT: J 92 LEU cc_start: 0.8799 (mm) cc_final: 0.8537 (mm) REVERT: J 97 ASP cc_start: 0.8452 (t0) cc_final: 0.8133 (t0) REVERT: J 99 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8006 (tm-30) REVERT: M 42 ASP cc_start: 0.9051 (p0) cc_final: 0.8674 (p0) REVERT: N 39 GLU cc_start: 0.9024 (tp30) cc_final: 0.8765 (tp30) REVERT: N 54 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8686 (t70) REVERT: S 29 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8583 (mmmt) outliers start: 20 outliers final: 16 residues processed: 145 average time/residue: 0.1354 time to fit residues: 29.8483 Evaluate side-chains 152 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 124 ARG Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain N residue 54 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 67 optimal weight: 0.0170 chunk 23 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 101 optimal weight: 0.3980 chunk 128 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 overall best weight: 3.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.044781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.033139 restraints weight = 129558.955| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.81 r_work: 0.2792 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19734 Z= 0.233 Angle : 0.600 13.506 28859 Z= 0.337 Chirality : 0.040 0.309 3602 Planarity : 0.004 0.037 1982 Dihedral : 21.670 178.277 8364 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.18 % Allowed : 17.25 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1084 helix: 1.15 (0.24), residues: 501 sheet: 0.53 (0.41), residues: 161 loop : -0.20 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 7 TYR 0.013 0.002 TYR C 168 PHE 0.020 0.002 PHE I 127 TRP 0.020 0.002 TRP B 104 HIS 0.005 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (19733) covalent geometry : angle 0.60044 / 0.34 (28859) hydrogen bonds : bond 0.06753 / 6.53 ( 758) hydrogen bonds : angle 4.07888 / 5.12 ( 1748) metal coordination : bond 0.00069 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.6746 (mmt) cc_final: 0.6097 (tpt) REVERT: B 100 MET cc_start: 0.9377 (tpp) cc_final: 0.9054 (tpp) REVERT: B 147 SER cc_start: 0.8820 (t) cc_final: 0.8579 (p) REVERT: I 124 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7977 (ptt90) REVERT: J 63 ASP cc_start: 0.8745 (t0) cc_final: 0.8468 (t0) REVERT: J 65 TYR cc_start: 0.9031 (m-80) cc_final: 0.8772 (m-80) REVERT: J 87 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9131 (pp) REVERT: J 92 LEU cc_start: 0.8735 (mm) cc_final: 0.8503 (mm) REVERT: J 97 ASP cc_start: 0.8461 (t0) cc_final: 0.8165 (t0) REVERT: J 99 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8130 (tm-30) REVERT: N 6 MET cc_start: 0.8251 (mmm) cc_final: 0.8043 (mmp) REVERT: N 39 GLU cc_start: 0.9122 (tp30) cc_final: 0.8848 (tp30) REVERT: N 54 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8701 (t70) outliers start: 20 outliers final: 16 residues processed: 138 average time/residue: 0.1335 time to fit residues: 27.8676 Evaluate side-chains 144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 124 ARG Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain N residue 54 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 96 optimal weight: 0.1980 chunk 42 optimal weight: 10.0000 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.045258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.033577 restraints weight = 130892.139| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.88 r_work: 0.2823 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19734 Z= 0.146 Angle : 0.562 13.878 28859 Z= 0.316 Chirality : 0.038 0.354 3602 Planarity : 0.004 0.035 1982 Dihedral : 21.695 178.750 8364 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 17.90 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.26), residues: 1084 helix: 1.18 (0.24), residues: 500 sheet: 0.59 (0.41), residues: 163 loop : -0.16 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 45 TYR 0.007 0.001 TYR M 86 PHE 0.011 0.001 PHE S 74 TRP 0.029 0.002 TRP B 104 HIS 0.023 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (19733) covalent geometry : angle 0.56158 / 0.32 (28859) hydrogen bonds : bond 0.05686 / 5.30 ( 758) hydrogen bonds : angle 3.96120 / 5.00 ( 1748) metal coordination : bond 0.00059 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5672.60 seconds wall clock time: 97 minutes 34.85 seconds (5854.85 seconds total)