Starting phenix.real_space_refine on Fri Aug 7 01:51:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h9m_51969/08_2026/9h9m_51969_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h9m_51969/08_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_51969/08_2026/9h9m_51969_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h9m_51969/08_2026/9h9m_51969_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h9m_51969/08_2026/9h9m_51969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h9m_51969/08_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-2.2rc3-6140/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: 3.84, per 1000 atoms: 0.21 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: 1.39 Conformation dependent library (CDL) restraints added in 338.1 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: 2.20 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: 4.20 Time building geometry restraints manager: 1.80 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: 28601 3.01 - 6.01: 213 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: 3292 0.100 - 0.199: 301 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: 4.850 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.750 Find NCS groups from input model: 0.080 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- 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= 0.308 Angle : 0.823 15.035 28859 Z= 0.590 Chirality : 0.052 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 0.00436 / 0.31 (19733) covalent geometry : angle 0.82314 / 0.59 (28859) hydrogen bonds : bond 0.17007 / 18.23 ( 758) hydrogen bonds : angle 6.20298 / 8.27 ( 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 : 0.464 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: symmetry clash REVERT: M 11 ASP cc_start: 0.6516 (p0) cc_final: 0.6219 (p0) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1525 time to fit residues: 39.5981 Evaluate side-chains 129 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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: 30.0000 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: 9.9990 chunk 149 optimal weight: 0.2980 overall best weight: 1.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 ASN G 68 ASN I 50 GLN I 126 GLN J 64 GLN M 8 ASN N 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.047031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.035224 restraints weight = 129730.381| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.00 r_work: 0.2900 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19734 Z= 0.142 Angle : 0.600 12.234 28859 Z= 0.339 Chirality : 0.041 0.539 3602 Planarity : 0.004 0.029 1982 Dihedral : 21.826 179.792 8364 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.42 % Allowed : 13.32 % Favored : 85.26 % 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: 0.67 (0.25), residues: 1084 helix: 0.90 (0.23), residues: 509 sheet: 0.59 (0.40), residues: 170 loop : -0.05 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 109 TYR 0.014 0.002 TYR I 38 PHE 0.021 0.002 PHE B 90 TRP 0.019 0.002 TRP B 23 HIS 0.009 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (19733) covalent geometry : angle 0.59978 / 0.34 (28859) hydrogen bonds : bond 0.07251 / 7.70 ( 758) hydrogen bonds : angle 4.35177 / 5.68 ( 1748) metal coordination : bond 0.00492 / 0.25 ( 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 170 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.474 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 100 MET cc_start: 0.9191 (tpp) cc_final: 0.8890 (tpp) REVERT: C 152 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7805 (tm-30) REVERT: C 165 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8814 (t) REVERT: G 136 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8456 (mmtm) REVERT: J 30 LYS cc_start: 0.9264 (mmmt) cc_final: 0.8864 (mmmt) REVERT: J 47 GLU cc_start: 0.8145 (mp0) cc_final: 0.7904 (mp0) REVERT: J 63 ASP cc_start: 0.8314 (t0) cc_final: 0.8060 (t0) REVERT: J 97 ASP cc_start: 0.8018 (t0) cc_final: 0.7809 (t0) REVERT: N 10 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8239 (tt0) outliers start: 13 outliers final: 8 residues processed: 163 average time/residue: 0.1621 time to fit residues: 39.2522 Evaluate side-chains 141 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 I residue 53 GLU 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: 0.0070 chunk 120 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 130 ASN I 110 GLN J 64 GLN M 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.045487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.033824 restraints weight = 132171.370| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.78 r_work: 0.2816 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19734 Z= 0.217 Angle : 0.634 9.865 28859 Z= 0.349 Chirality : 0.044 0.290 3602 Planarity : 0.005 0.032 1982 Dihedral : 21.645 179.103 8364 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.62 % Allowed : 14.19 % Favored : 83.19 % 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: 0.59 (0.25), residues: 1084 helix: 1.01 (0.23), residues: 500 sheet: 0.47 (0.40), residues: 162 loop : -0.27 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 132 TYR 0.026 0.002 TYR C 168 PHE 0.016 0.002 PHE B 90 TRP 0.018 0.002 TRP G 103 HIS 0.012 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.22 (19733) covalent geometry : angle 0.63394 / 0.35 (28859) hydrogen bonds : bond 0.07753 / 8.28 ( 758) hydrogen bonds : angle 4.20795 / 5.48 ( 1748) metal coordination : bond 0.00153 / 0.08 ( 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 162 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.460 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: 0.9339 (tpp) cc_final: 0.8978 (tpp) REVERT: B 168 HIS cc_start: 0.8706 (t-170) cc_final: 0.8499 (t-170) REVERT: C 152 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7797 (tm-30) REVERT: G 136 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8438 (mmtm) REVERT: J 30 LYS cc_start: 0.9289 (mmmt) cc_final: 0.8928 (mmmt) REVERT: J 47 GLU cc_start: 0.8173 (mp0) cc_final: 0.7952 (mp0) REVERT: J 63 ASP cc_start: 0.8702 (t0) cc_final: 0.8221 (t0) REVERT: J 64 GLN cc_start: 0.8937 (mt0) cc_final: 0.8678 (mt0) REVERT: J 66 GLU cc_start: 0.9005 (tt0) cc_final: 0.8562 (tm-30) REVERT: J 97 ASP cc_start: 0.8216 (t0) cc_final: 0.7977 (t0) REVERT: J 99 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7857 (tm-30) REVERT: M 27 LYS cc_start: 0.9090 (tppp) cc_final: 0.8881 (tppt) REVERT: N 10 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: N 39 GLU cc_start: 0.9009 (tp30) cc_final: 0.8778 (tp30) outliers start: 24 outliers final: 12 residues processed: 150 average time/residue: 0.1531 time to fit residues: 34.7978 Evaluate side-chains 140 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.045813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.034166 restraints weight = 131403.809| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.78 r_work: 0.2835 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19734 Z= 0.152 Angle : 0.550 8.708 28859 Z= 0.312 Chirality : 0.038 0.285 3602 Planarity : 0.004 0.076 1982 Dihedral : 21.634 178.942 8364 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.97 % Allowed : 14.74 % Favored : 83.30 % 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: 0.76 (0.25), residues: 1084 helix: 1.20 (0.24), residues: 501 sheet: 0.60 (0.40), residues: 162 loop : -0.28 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 108 TYR 0.015 0.002 TYR C 168 PHE 0.009 0.001 PHE C 130 TRP 0.031 0.002 TRP B 104 HIS 0.003 0.001 HIS S 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (19733) covalent geometry : angle 0.54962 / 0.31 (28859) hydrogen bonds : bond 0.06223 / 6.45 ( 758) hydrogen bonds : angle 3.97402 / 5.18 ( 1748) metal coordination : bond 0.00250 / 0.12 ( 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 156 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.474 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: 0.9344 (tpp) cc_final: 0.8992 (tpp) REVERT: G 136 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8514 (mmtm) REVERT: J 47 GLU cc_start: 0.8170 (mp0) cc_final: 0.7965 (mp0) REVERT: J 97 ASP cc_start: 0.8264 (t0) cc_final: 0.7969 (t0) REVERT: J 99 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7887 (tm-30) REVERT: N 6 MET cc_start: 0.8068 (mmp) cc_final: 0.7835 (mmp) REVERT: N 39 GLU cc_start: 0.9001 (tp30) cc_final: 0.8772 (tp30) REVERT: N 89 MET cc_start: 0.8946 (mmm) cc_final: 0.8726 (mmm) outliers start: 18 outliers final: 11 residues processed: 146 average time/residue: 0.1529 time to fit residues: 33.6757 Evaluate side-chains 137 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 M residue 89 LEU 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: 6.9990 chunk 115 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS G 130 ASN J 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.045168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.033534 restraints weight = 131390.838| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.67 r_work: 0.2810 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19734 Z= 0.199 Angle : 0.587 10.687 28859 Z= 0.325 Chirality : 0.042 0.399 3602 Planarity : 0.004 0.056 1982 Dihedral : 21.608 178.855 8364 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.28 % Allowed : 14.19 % Favored : 82.53 % 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: 1.11 (0.23), residues: 500 sheet: 0.49 (0.40), residues: 162 loop : -0.24 (0.29), residues: 422 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 0.012 0.001 PHE S 74 TRP 0.038 0.002 TRP B 104 HIS 0.019 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (19733) covalent geometry : angle 0.58727 / 0.33 (28859) hydrogen bonds : bond 0.06763 / 7.12 ( 758) hydrogen bonds : angle 3.98364 / 5.19 ( 1748) metal coordination : bond 0.00172 / 0.09 ( 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 161 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.388 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: 0.9362 (tpp) cc_final: 0.8995 (tpp) REVERT: G 136 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8509 (mmtm) REVERT: J 63 ASP cc_start: 0.8802 (t0) cc_final: 0.8443 (t0) REVERT: J 97 ASP cc_start: 0.8369 (t0) cc_final: 0.8066 (t0) REVERT: J 99 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8046 (tm-30) REVERT: N 6 MET cc_start: 0.8070 (mmp) cc_final: 0.7797 (mmp) REVERT: N 39 GLU cc_start: 0.9081 (tp30) cc_final: 0.8799 (tp30) REVERT: N 54 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8762 (t70) REVERT: N 89 MET cc_start: 0.8923 (mmm) cc_final: 0.8699 (mmm) outliers start: 30 outliers final: 13 residues processed: 149 average time/residue: 0.1414 time to fit residues: 31.8546 Evaluate side-chains 138 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.0870 chunk 88 optimal weight: 0.0020 chunk 55 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 0.3980 chunk 75 optimal weight: 0.3980 chunk 20 optimal weight: 20.0000 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN B 168 HIS J 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.046267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.034621 restraints weight = 128409.517| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.90 r_work: 0.2864 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19734 Z= 0.111 Angle : 0.519 8.624 28859 Z= 0.296 Chirality : 0.035 0.270 3602 Planarity : 0.004 0.034 1982 Dihedral : 21.618 179.176 8364 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.97 % Allowed : 15.72 % Favored : 82.31 % 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: 0.95 (0.26), residues: 1084 helix: 1.30 (0.24), residues: 494 sheet: 0.78 (0.40), residues: 161 loop : -0.10 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 57 TYR 0.015 0.002 TYR C 168 PHE 0.026 0.001 PHE I 127 TRP 0.028 0.002 TRP B 104 HIS 0.012 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (19733) covalent geometry : angle 0.51934 / 0.30 (28859) hydrogen bonds : bond 0.05440 / 5.50 ( 758) hydrogen bonds : angle 3.80369 / 4.98 ( 1748) metal coordination : bond 0.00212 / 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 164 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.498 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: 0.9338 (tpp) cc_final: 0.8973 (tpp) REVERT: G 136 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8580 (mmtm) REVERT: J 30 LYS cc_start: 0.9314 (mmmt) cc_final: 0.9024 (mmmt) REVERT: J 63 ASP cc_start: 0.8783 (t0) cc_final: 0.8468 (t0) REVERT: J 64 GLN cc_start: 0.8835 (mt0) cc_final: 0.8590 (mt0) REVERT: J 97 ASP cc_start: 0.8361 (t0) cc_final: 0.8022 (t0) REVERT: J 99 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7932 (tm-30) REVERT: M 42 ASP cc_start: 0.9018 (p0) cc_final: 0.8509 (p0) REVERT: N 39 GLU cc_start: 0.8998 (tp30) cc_final: 0.8714 (tp30) REVERT: N 54 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8669 (t70) outliers start: 18 outliers final: 10 residues processed: 153 average time/residue: 0.1503 time to fit residues: 35.1340 Evaluate side-chains 143 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 11 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 134 optimal weight: 0.0970 chunk 152 optimal weight: 6.9990 chunk 149 optimal weight: 0.0170 chunk 99 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.7818 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.046457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.034740 restraints weight = 130451.367| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.99 r_work: 0.2880 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2958 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= 0.109 Angle : 0.529 13.362 28859 Z= 0.295 Chirality : 0.035 0.235 3602 Planarity : 0.004 0.036 1982 Dihedral : 21.561 179.212 8364 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.86 % Allowed : 17.14 % Favored : 81.00 % 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: 0.98 (0.26), residues: 1084 helix: 1.26 (0.24), residues: 493 sheet: 0.88 (0.41), residues: 161 loop : -0.05 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.017 0.002 TYR C 168 PHE 0.006 0.001 PHE S 74 TRP 0.026 0.001 TRP B 104 HIS 0.011 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (19733) covalent geometry : angle 0.52855 / 0.30 (28859) hydrogen bonds : bond 0.05324 / 5.37 ( 758) hydrogen bonds : angle 3.79027 / 4.98 ( 1748) metal coordination : bond 0.00177 / 0.09 ( 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 162 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.483 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: 0.9322 (tpp) cc_final: 0.8950 (tpp) REVERT: B 147 SER cc_start: 0.8758 (t) cc_final: 0.8512 (p) REVERT: C 129 MET cc_start: 0.7738 (tmm) cc_final: 0.7520 (tmm) REVERT: G 136 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8542 (mmtm) REVERT: J 30 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8996 (mmmt) REVERT: J 63 ASP cc_start: 0.8749 (t0) cc_final: 0.8443 (t0) REVERT: J 97 ASP cc_start: 0.8376 (t0) cc_final: 0.8026 (t0) REVERT: J 99 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8000 (tm-30) REVERT: M 42 ASP cc_start: 0.8925 (p0) cc_final: 0.8647 (p0) REVERT: N 39 GLU cc_start: 0.9003 (tp30) cc_final: 0.8717 (tp30) outliers start: 17 outliers final: 10 residues processed: 153 average time/residue: 0.1560 time to fit residues: 36.1087 Evaluate side-chains 144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain I residue 35 LEU 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 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: 20.0000 chunk 135 optimal weight: 0.4980 chunk 150 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 54 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS J 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.046518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.034728 restraints weight = 129850.953| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.88 r_work: 0.2892 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19734 Z= 0.113 Angle : 0.539 13.927 28859 Z= 0.298 Chirality : 0.036 0.333 3602 Planarity : 0.004 0.036 1982 Dihedral : 21.537 179.190 8364 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.53 % Allowed : 17.90 % Favored : 80.57 % 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: 0.97 (0.26), residues: 1084 helix: 1.19 (0.24), residues: 498 sheet: 0.93 (0.41), residues: 161 loop : 0.01 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 7 TYR 0.017 0.002 TYR C 168 PHE 0.023 0.001 PHE I 127 TRP 0.021 0.001 TRP B 104 HIS 0.011 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (19733) covalent geometry : angle 0.53855 / 0.30 (28859) hydrogen bonds : bond 0.05335 / 5.41 ( 758) hydrogen bonds : angle 3.79447 / 5.03 ( 1748) metal coordination : bond 0.00162 / 0.08 ( 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 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.6873 (mmt) cc_final: 0.6202 (tpt) REVERT: B 100 MET cc_start: 0.9307 (tpp) cc_final: 0.8960 (tpp) REVERT: B 147 SER cc_start: 0.8806 (t) cc_final: 0.8537 (p) REVERT: G 103 TRP cc_start: 0.9210 (m-10) cc_final: 0.8468 (m-10) REVERT: G 135 VAL cc_start: 0.6941 (OUTLIER) cc_final: 0.6666 (m) REVERT: G 136 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8547 (mmtm) REVERT: J 30 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8964 (mmmt) REVERT: J 63 ASP cc_start: 0.8742 (t0) cc_final: 0.8452 (t0) REVERT: J 90 LEU cc_start: 0.8531 (mt) cc_final: 0.8295 (mp) REVERT: J 97 ASP cc_start: 0.8373 (t0) cc_final: 0.8034 (t0) REVERT: J 99 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7985 (tm-30) REVERT: M 42 ASP cc_start: 0.9014 (p0) cc_final: 0.8542 (p0) REVERT: N 39 GLU cc_start: 0.8953 (tp30) cc_final: 0.8668 (tp30) outliers start: 14 outliers final: 12 residues processed: 149 average time/residue: 0.1538 time to fit residues: 34.5663 Evaluate side-chains 147 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain I residue 35 LEU 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 28 THR 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: 8.9990 chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS J 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.044256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.032705 restraints weight = 132632.088| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.69 r_work: 0.2767 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 19734 Z= 0.351 Angle : 0.778 13.288 28859 Z= 0.407 Chirality : 0.052 0.360 3602 Planarity : 0.006 0.050 1982 Dihedral : 21.576 178.291 8364 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.51 % Allowed : 17.90 % Favored : 79.59 % 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: 0.41 (0.25), residues: 1084 helix: 0.88 (0.23), residues: 498 sheet: 0.28 (0.40), residues: 161 loop : -0.34 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 45 TYR 0.021 0.003 TYR C 168 PHE 0.017 0.003 PHE S 74 TRP 0.021 0.002 TRP B 104 HIS 0.025 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.35 (19733) covalent geometry : angle 0.77829 / 0.41 (28859) hydrogen bonds : bond 0.08832 / 9.54 ( 758) hydrogen bonds : angle 4.31405 / 5.69 ( 1748) metal coordination : bond 0.00078 / 0.04 ( 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 140 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.6705 (mmt) cc_final: 0.5996 (tpt) REVERT: B 100 MET cc_start: 0.9360 (tpp) cc_final: 0.9024 (tpp) REVERT: B 147 SER cc_start: 0.8824 (t) cc_final: 0.8569 (p) REVERT: C 168 TYR cc_start: 0.8696 (t80) cc_final: 0.8477 (t80) REVERT: J 63 ASP cc_start: 0.8763 (t0) cc_final: 0.8544 (t0) REVERT: J 90 LEU cc_start: 0.8415 (mt) cc_final: 0.8138 (mp) REVERT: J 97 ASP cc_start: 0.8491 (t0) cc_final: 0.8180 (t0) REVERT: N 39 GLU cc_start: 0.9173 (tp30) cc_final: 0.8905 (tp30) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.1515 time to fit residues: 30.1109 Evaluate side-chains 133 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 168 HIS 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 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 87 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain N residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 67 optimal weight: 0.0010 chunk 23 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS J 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.045240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.033619 restraints weight = 130641.308| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.72 r_work: 0.2825 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19734 Z= 0.135 Angle : 0.588 11.717 28859 Z= 0.329 Chirality : 0.038 0.279 3602 Planarity : 0.004 0.034 1982 Dihedral : 21.585 178.616 8364 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.64 % Allowed : 19.21 % Favored : 79.15 % 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: 0.66 (0.26), residues: 1084 helix: 1.05 (0.24), residues: 500 sheet: 0.48 (0.41), residues: 161 loop : -0.19 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 5 TYR 0.017 0.002 TYR C 168 PHE 0.027 0.001 PHE I 127 TRP 0.035 0.002 TRP B 104 HIS 0.030 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (19733) covalent geometry : angle 0.58765 / 0.33 (28859) hydrogen bonds : bond 0.06069 / 6.24 ( 758) hydrogen bonds : angle 3.96514 / 5.25 ( 1748) metal coordination : bond 0.00097 / 0.05 ( 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 143 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.407 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 6 MET cc_start: 0.6772 (mmt) cc_final: 0.6092 (tpt) REVERT: B 100 MET cc_start: 0.9362 (tpp) cc_final: 0.9027 (tpp) REVERT: B 147 SER cc_start: 0.8851 (t) cc_final: 0.8597 (p) REVERT: C 168 TYR cc_start: 0.8634 (t80) cc_final: 0.8430 (t80) REVERT: J 63 ASP cc_start: 0.8739 (t0) cc_final: 0.8531 (t0) REVERT: J 87 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9149 (pp) REVERT: J 97 ASP cc_start: 0.8420 (t0) cc_final: 0.8097 (t0) REVERT: J 99 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7897 (tm-30) REVERT: N 39 GLU cc_start: 0.9064 (tp30) cc_final: 0.8827 (tp30) REVERT: S 29 LYS cc_start: 0.9077 (mmmt) cc_final: 0.8591 (mmmt) outliers start: 15 outliers final: 14 residues processed: 136 average time/residue: 0.1457 time to fit residues: 30.1927 Evaluate side-chains 139 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 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 87 LEU Chi-restraints excluded: chain N residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 33 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 134 optimal weight: 0.0980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 chunk 96 optimal weight: 0.0170 chunk 42 optimal weight: 9.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS J 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.046330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.034677 restraints weight = 131203.610| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.04 r_work: 0.2884 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19734 Z= 0.115 Angle : 0.557 11.222 28859 Z= 0.310 Chirality : 0.036 0.221 3602 Planarity : 0.004 0.038 1982 Dihedral : 21.543 179.170 8364 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.97 % Allowed : 18.67 % Favored : 79.37 % 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: 0.77 (0.26), residues: 1084 helix: 1.09 (0.24), residues: 500 sheet: 0.59 (0.42), residues: 165 loop : -0.09 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 5 TYR 0.016 0.001 TYR C 168 PHE 0.010 0.001 PHE S 74 TRP 0.031 0.002 TRP B 104 HIS 0.015 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (19733) covalent geometry : angle 0.55661 / 0.31 (28859) hydrogen bonds : bond 0.05258 / 5.31 ( 758) hydrogen bonds : angle 3.89066 / 5.21 ( 1748) metal coordination : bond 0.00062 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6082.75 seconds wall clock time: 104 minutes 33.29 seconds (6273.29 seconds total)