Starting phenix.real_space_refine on Thu Sep 18 17:20:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h9m_51969/09_2025/9h9m_51969_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h9m_51969/09_2025/9h9m_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_51969/09_2025/9h9m_51969_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h9m_51969/09_2025/9h9m_51969_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h9m_51969/09_2025/9h9m_51969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h9m_51969/09_2025/9h9m_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-2.0-5805/lib/python3.9/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: 4.63, per 1000 atoms: 0.25 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: 1.81 Conformation dependent library (CDL) restraints added in 505.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.06 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: 4.39 Time building geometry restraints manager: 2.43 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.740 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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= 0.233 Angle : 0.712 15.035 28859 Z= 0.402 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 aren 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 covalent geometry : bond 0.00416 (19733) covalent geometry : angle 0.71197 (28859) hydrogen bonds : bond 0.17007 ( 758) hydrogen bonds : angle 6.20298 ( 1748) metal coordination : bond 0.09449 ( 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 : 0.476 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: 0.1695 time to fit residues: 43.7164 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 : 0.453 ------------------------------------------------------------------------------- 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: B 190 ASN G 68 ASN I 50 GLN I 110 GLN I 126 GLN J 56 HIS J 64 GLN M 8 ASN N 43 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.047491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.035656 restraints weight = 129473.046| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.07 r_work: 0.2927 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19734 Z= 0.127 Angle : 0.599 10.093 28859 Z= 0.315 Chirality : 0.037 0.269 3602 Planarity : 0.004 0.030 1982 Dihedral : 21.751 179.321 8364 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.86 % Allowed : 12.12 % Favored : 86.03 % 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 aren not related in a simple way. whole: 1.01 (0.25), residues: 1084 helix: 1.24 (0.23), residues: 507 sheet: 0.89 (0.40), residues: 162 loop : -0.01 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 132 TYR 0.014 0.002 TYR C 168 PHE 0.016 0.001 PHE B 90 TRP 0.020 0.002 TRP B 23 HIS 0.010 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00252 (19733) covalent geometry : angle 0.59862 (28859) hydrogen bonds : bond 0.05254 ( 758) hydrogen bonds : angle 3.90716 ( 1748) metal coordination : bond 0.00080 ( 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 184 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.281 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: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.9072 (mmm) cc_final: 0.8872 (tpp) REVERT: C 152 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 165 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8824 (t) REVERT: C 185 ASN cc_start: 0.9131 (t0) cc_final: 0.8911 (t0) REVERT: G 103 TRP cc_start: 0.8857 (m-10) cc_final: 0.8427 (m-10) REVERT: G 136 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8477 (mmtm) REVERT: J 30 LYS cc_start: 0.9289 (mmmt) cc_final: 0.9000 (mmmt) REVERT: J 47 GLU cc_start: 0.8195 (mp0) cc_final: 0.7909 (mp0) REVERT: J 63 ASP cc_start: 0.8188 (t0) cc_final: 0.7977 (t0) REVERT: J 64 GLN cc_start: 0.8330 (mt0) cc_final: 0.8100 (mt0) REVERT: J 68 ARG cc_start: 0.8847 (mtp85) cc_final: 0.8635 (mtt180) REVERT: M 42 ASP cc_start: 0.8610 (p0) cc_final: 0.8227 (p0) REVERT: S 21 LYS cc_start: 0.9223 (mmtm) cc_final: 0.8847 (mmtm) outliers start: 17 outliers final: 5 residues processed: 172 average time/residue: 0.1404 time to fit residues: 35.7524 Evaluate side-chains 146 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 GLN 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 51 VAL Chi-restraints excluded: chain M residue 34 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 119 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 76 optimal weight: 0.1980 chunk 141 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 130 ASN I 110 GLN ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.045129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.033146 restraints weight = 132496.738| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.76 r_work: 0.2815 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19734 Z= 0.220 Angle : 0.604 8.690 28859 Z= 0.317 Chirality : 0.038 0.263 3602 Planarity : 0.004 0.036 1982 Dihedral : 21.695 177.611 8364 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.29 % Allowed : 13.97 % Favored : 83.73 % 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 aren not related in a simple way. whole: 1.02 (0.25), residues: 1084 helix: 1.28 (0.23), residues: 511 sheet: 0.73 (0.40), residues: 164 loop : 0.02 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 132 TYR 0.020 0.002 TYR C 168 PHE 0.013 0.002 PHE B 90 TRP 0.027 0.002 TRP B 104 HIS 0.005 0.001 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00439 (19733) covalent geometry : angle 0.60440 (28859) hydrogen bonds : bond 0.06120 ( 758) hydrogen bonds : angle 3.98400 ( 1748) metal coordination : bond 0.00118 ( 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 165 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.9110 (mmm) cc_final: 0.8881 (tpp) REVERT: B 100 MET cc_start: 0.9316 (tpp) cc_final: 0.8935 (tpp) REVERT: C 152 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7843 (tm-30) REVERT: G 103 TRP cc_start: 0.9097 (m-10) cc_final: 0.8358 (m-10) REVERT: G 136 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8496 (mmtm) REVERT: J 30 LYS cc_start: 0.9313 (mmmt) cc_final: 0.9027 (mmmt) REVERT: J 54 SER cc_start: 0.9197 (t) cc_final: 0.8953 (t) REVERT: N 54 ASP cc_start: 0.9102 (m-30) cc_final: 0.8787 (t70) REVERT: S 21 LYS cc_start: 0.9162 (mmtm) cc_final: 0.8663 (mmtm) outliers start: 21 outliers final: 8 residues processed: 156 average time/residue: 0.1511 time to fit residues: 35.2777 Evaluate side-chains 138 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 154 SER 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 66 GLU Chi-restraints excluded: chain M residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 108 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3352 r_free = 0.3352 target = 0.044340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.032606 restraints weight = 133375.775| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.04 r_work: 0.2780 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 19734 Z= 0.280 Angle : 0.625 8.568 28859 Z= 0.329 Chirality : 0.039 0.267 3602 Planarity : 0.004 0.038 1982 Dihedral : 21.674 177.976 8364 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.29 % Allowed : 14.96 % Favored : 82.75 % 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 aren not related in a simple way. whole: 0.77 (0.25), residues: 1084 helix: 1.11 (0.23), residues: 513 sheet: 0.63 (0.41), residues: 161 loop : -0.17 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 90 TYR 0.016 0.002 TYR C 168 PHE 0.014 0.002 PHE S 74 TRP 0.024 0.002 TRP B 104 HIS 0.005 0.001 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00556 (19733) covalent geometry : angle 0.62528 (28859) hydrogen bonds : bond 0.06346 ( 758) hydrogen bonds : angle 3.97692 ( 1748) metal coordination : bond 0.00070 ( 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 155 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5947 (tpp) REVERT: B 49 MET cc_start: 0.9138 (mmm) cc_final: 0.8920 (tpp) REVERT: B 100 MET cc_start: 0.9354 (tpp) cc_final: 0.9064 (tpp) REVERT: B 147 SER cc_start: 0.8723 (t) cc_final: 0.8475 (p) REVERT: G 135 VAL cc_start: 0.6944 (OUTLIER) cc_final: 0.6616 (m) REVERT: G 136 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8608 (mmtm) REVERT: N 39 GLU cc_start: 0.9099 (tp30) cc_final: 0.8834 (tp30) REVERT: N 54 ASP cc_start: 0.9132 (m-30) cc_final: 0.8917 (t0) REVERT: S 21 LYS cc_start: 0.9075 (mmtm) cc_final: 0.8868 (mmtm) outliers start: 21 outliers final: 8 residues processed: 147 average time/residue: 0.1464 time to fit residues: 32.9907 Evaluate side-chains 134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 135 VAL 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 M residue 34 LEU Chi-restraints excluded: chain N residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 117 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN I 37 GLN I 110 GLN J 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.044990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.033522 restraints weight = 130397.685| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.65 r_work: 0.2808 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19734 Z= 0.191 Angle : 0.567 10.186 28859 Z= 0.298 Chirality : 0.037 0.242 3602 Planarity : 0.004 0.037 1982 Dihedral : 21.615 177.472 8364 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.62 % Allowed : 15.94 % Favored : 81.44 % 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 aren not related in a simple way. whole: 0.99 (0.26), residues: 1084 helix: 1.30 (0.23), residues: 513 sheet: 0.69 (0.41), residues: 161 loop : -0.06 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 4 TYR 0.016 0.002 TYR C 168 PHE 0.010 0.001 PHE S 74 TRP 0.020 0.002 TRP B 104 HIS 0.003 0.001 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00379 (19733) covalent geometry : angle 0.56712 (28859) hydrogen bonds : bond 0.05281 ( 758) hydrogen bonds : angle 3.80522 ( 1748) metal coordination : bond 0.00036 ( 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 165 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.419 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: 0.9398 (tpp) cc_final: 0.9065 (tpp) REVERT: B 147 SER cc_start: 0.8785 (t) cc_final: 0.8536 (p) REVERT: J 63 ASP cc_start: 0.8761 (t0) cc_final: 0.8489 (t0) REVERT: J 64 GLN cc_start: 0.8861 (mt0) cc_final: 0.8637 (mt0) REVERT: J 65 TYR cc_start: 0.8948 (m-80) cc_final: 0.8699 (m-80) REVERT: J 87 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9159 (pp) REVERT: J 99 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8019 (tm-30) REVERT: M 27 LYS cc_start: 0.8989 (tppp) cc_final: 0.8783 (tppt) REVERT: M 42 ASP cc_start: 0.8960 (p0) cc_final: 0.8509 (p0) REVERT: N 39 GLU cc_start: 0.9087 (tp30) cc_final: 0.8745 (tp30) REVERT: N 54 ASP cc_start: 0.9055 (m-30) cc_final: 0.8822 (t0) REVERT: S 21 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8872 (mmtm) outliers start: 24 outliers final: 10 residues processed: 151 average time/residue: 0.1385 time to fit residues: 31.5252 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 : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain G residue 5 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 124 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 ASN C 139 GLN I 110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.045073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.033582 restraints weight = 130703.703| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.78 r_work: 0.2823 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19734 Z= 0.169 Angle : 0.565 9.695 28859 Z= 0.296 Chirality : 0.036 0.248 3602 Planarity : 0.004 0.034 1982 Dihedral : 21.589 177.692 8364 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.29 % Allowed : 16.59 % Favored : 81.11 % 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 aren not related in a simple way. whole: 1.03 (0.26), residues: 1084 helix: 1.32 (0.24), residues: 507 sheet: 0.83 (0.42), residues: 161 loop : -0.05 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 5 TYR 0.019 0.001 TYR C 168 PHE 0.017 0.001 PHE I 127 TRP 0.017 0.001 TRP B 104 HIS 0.003 0.001 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00339 (19733) covalent geometry : angle 0.56502 (28859) hydrogen bonds : bond 0.05094 ( 758) hydrogen bonds : angle 3.74721 ( 1748) metal coordination : bond 0.00274 ( 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 158 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9371 (tpp) cc_final: 0.9041 (tpp) REVERT: B 147 SER cc_start: 0.8803 (t) cc_final: 0.8551 (p) REVERT: J 63 ASP cc_start: 0.8751 (t0) cc_final: 0.8424 (t0) REVERT: J 64 GLN cc_start: 0.8910 (mt0) cc_final: 0.8658 (mt0) REVERT: J 87 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9112 (pp) REVERT: M 27 LYS cc_start: 0.8990 (tppp) cc_final: 0.8788 (tppt) REVERT: M 42 ASP cc_start: 0.8981 (p0) cc_final: 0.8575 (p0) REVERT: N 39 GLU cc_start: 0.9095 (tp30) cc_final: 0.8729 (tp30) REVERT: N 54 ASP cc_start: 0.9060 (m-30) cc_final: 0.8807 (t0) REVERT: N 89 MET cc_start: 0.8955 (mmm) cc_final: 0.8722 (mmm) REVERT: S 21 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8813 (mmtm) outliers start: 21 outliers final: 14 residues processed: 148 average time/residue: 0.1532 time to fit residues: 34.6664 Evaluate side-chains 140 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 149 ILE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR 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 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 M residue 91 HIS 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: 8.9990 chunk 43 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN I 110 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.043986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.032452 restraints weight = 131982.923| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.87 r_work: 0.2756 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19734 Z= 0.306 Angle : 0.663 9.281 28859 Z= 0.343 Chirality : 0.040 0.237 3602 Planarity : 0.004 0.035 1982 Dihedral : 21.656 177.909 8364 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.40 % Allowed : 18.56 % Favored : 79.04 % 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 aren not related in a simple way. whole: 0.68 (0.26), residues: 1084 helix: 1.12 (0.23), residues: 506 sheet: 0.51 (0.41), residues: 161 loop : -0.28 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 59 TYR 0.019 0.002 TYR C 168 PHE 0.013 0.002 PHE S 74 TRP 0.016 0.002 TRP B 104 HIS 0.006 0.001 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00607 (19733) covalent geometry : angle 0.66330 (28859) hydrogen bonds : bond 0.06565 ( 758) hydrogen bonds : angle 4.02058 ( 1748) metal coordination : bond 0.00057 ( 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 144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9378 (tpp) cc_final: 0.9076 (tpp) REVERT: B 147 SER cc_start: 0.8891 (t) cc_final: 0.8642 (p) REVERT: G 5 ARG cc_start: 0.9039 (ptt-90) cc_final: 0.8760 (ptp90) REVERT: J 87 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9083 (pp) REVERT: M 27 LYS cc_start: 0.9093 (tppp) cc_final: 0.8731 (tppt) REVERT: M 28 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9142 (p) REVERT: M 31 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8905 (mtmm) REVERT: N 39 GLU cc_start: 0.9133 (tp30) cc_final: 0.8858 (tp30) REVERT: S 21 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8832 (mmtm) outliers start: 22 outliers final: 15 residues processed: 136 average time/residue: 0.1384 time to fit residues: 28.9945 Evaluate side-chains 134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 69 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 135 optimal weight: 0.4980 chunk 150 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN I 110 GLN J 20 GLN J 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.045607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.034236 restraints weight = 130575.528| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.85 r_work: 0.2849 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19734 Z= 0.117 Angle : 0.554 10.352 28859 Z= 0.290 Chirality : 0.035 0.253 3602 Planarity : 0.003 0.032 1982 Dihedral : 21.583 178.001 8364 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.07 % Allowed : 19.32 % Favored : 78.60 % 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 aren not related in a simple way. whole: 1.07 (0.26), residues: 1084 helix: 1.43 (0.24), residues: 498 sheet: 0.50 (0.40), residues: 175 loop : 0.04 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 45 TYR 0.018 0.002 TYR C 168 PHE 0.028 0.001 PHE I 127 TRP 0.027 0.002 TRP B 104 HIS 0.002 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00237 (19733) covalent geometry : angle 0.55420 (28859) hydrogen bonds : bond 0.04545 ( 758) hydrogen bonds : angle 3.68894 ( 1748) metal coordination : bond 0.00033 ( 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 159 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9424 (tpp) cc_final: 0.9103 (tpp) REVERT: B 147 SER cc_start: 0.8930 (t) cc_final: 0.8634 (p) REVERT: C 185 ASN cc_start: 0.9128 (t0) cc_final: 0.8911 (t0) REVERT: J 63 ASP cc_start: 0.8727 (t0) cc_final: 0.8449 (t0) REVERT: J 87 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9035 (pp) REVERT: M 42 ASP cc_start: 0.8974 (p0) cc_final: 0.8601 (p0) REVERT: N 39 GLU cc_start: 0.9082 (tp30) cc_final: 0.8766 (tp30) REVERT: N 89 MET cc_start: 0.8958 (mmm) cc_final: 0.8742 (mmm) outliers start: 19 outliers final: 13 residues processed: 149 average time/residue: 0.1306 time to fit residues: 29.8926 Evaluate side-chains 144 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 88 MET 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 M residue 91 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 43 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 128 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 51 optimal weight: 40.0000 overall best weight: 1.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 GLN J 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.045267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.033665 restraints weight = 131501.075| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.17 r_work: 0.2840 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19734 Z= 0.147 Angle : 0.571 9.989 28859 Z= 0.296 Chirality : 0.035 0.241 3602 Planarity : 0.004 0.032 1982 Dihedral : 21.518 178.113 8364 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.40 % Allowed : 19.54 % Favored : 78.06 % 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 aren not related in a simple way. whole: 1.06 (0.26), residues: 1084 helix: 1.41 (0.24), residues: 500 sheet: 0.42 (0.40), residues: 179 loop : 0.08 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 138 TYR 0.006 0.001 TYR C 168 PHE 0.010 0.001 PHE B 90 TRP 0.020 0.001 TRP B 104 HIS 0.003 0.001 HIS B 94 Details of bonding type rmsd covalent geometry : bond 0.00297 (19733) covalent geometry : angle 0.57121 (28859) hydrogen bonds : bond 0.04803 ( 758) hydrogen bonds : angle 3.74487 ( 1748) metal coordination : bond 0.00009 ( 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 154 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.324 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: 0.9382 (tpp) cc_final: 0.9042 (tpp) REVERT: B 147 SER cc_start: 0.8890 (t) cc_final: 0.8613 (p) REVERT: C 185 ASN cc_start: 0.9150 (t0) cc_final: 0.8915 (t0) REVERT: G 7 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7363 (tp) REVERT: J 63 ASP cc_start: 0.8673 (t0) cc_final: 0.8429 (t0) REVERT: J 99 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7822 (tm-30) REVERT: M 42 ASP cc_start: 0.8992 (p0) cc_final: 0.8610 (p0) REVERT: N 39 GLU cc_start: 0.9077 (tp30) cc_final: 0.8778 (tp30) REVERT: N 54 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8499 (t70) REVERT: N 89 MET cc_start: 0.8974 (mmm) cc_final: 0.8729 (mmm) outliers start: 22 outliers final: 15 residues processed: 140 average time/residue: 0.1353 time to fit residues: 29.5605 Evaluate side-chains 145 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 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 5 ARG Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 88 MET Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 91 HIS 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: 7.9990 chunk 41 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.044622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.033043 restraints weight = 131148.801| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.10 r_work: 0.2798 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19734 Z= 0.206 Angle : 0.613 12.649 28859 Z= 0.317 Chirality : 0.036 0.200 3602 Planarity : 0.004 0.032 1982 Dihedral : 21.501 177.433 8364 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.97 % Allowed : 19.98 % Favored : 78.06 % 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 aren not related in a simple way. whole: 0.99 (0.26), residues: 1084 helix: 1.38 (0.24), residues: 499 sheet: 0.33 (0.40), residues: 177 loop : 0.06 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 138 TYR 0.008 0.001 TYR N 20 PHE 0.029 0.001 PHE I 127 TRP 0.021 0.002 TRP B 104 HIS 0.003 0.001 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00413 (19733) covalent geometry : angle 0.61255 (28859) hydrogen bonds : bond 0.05543 ( 758) hydrogen bonds : angle 3.94184 ( 1748) metal coordination : bond 0.00034 ( 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 145 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 MET cc_start: 0.9419 (tpp) cc_final: 0.9067 (tpp) REVERT: B 147 SER cc_start: 0.8883 (t) cc_final: 0.8593 (p) REVERT: J 63 ASP cc_start: 0.8667 (t0) cc_final: 0.8418 (t0) REVERT: J 99 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7882 (tm-30) REVERT: M 42 ASP cc_start: 0.9026 (p0) cc_final: 0.8666 (p0) REVERT: N 39 GLU cc_start: 0.9085 (tp30) cc_final: 0.8794 (tp30) REVERT: N 54 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8582 (t70) REVERT: N 89 MET cc_start: 0.9023 (mmm) cc_final: 0.8774 (mmm) outliers start: 18 outliers final: 15 residues processed: 137 average time/residue: 0.1270 time to fit residues: 27.0289 Evaluate side-chains 139 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ILE Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 41 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 5 ARG Chi-restraints excluded: chain I residue 28 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 J residue 42 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 91 HIS 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: 7.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN J 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.043207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.031561 restraints weight = 134419.637| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.13 r_work: 0.2747 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 19734 Z= 0.394 Angle : 0.756 11.988 28859 Z= 0.388 Chirality : 0.043 0.216 3602 Planarity : 0.005 0.040 1982 Dihedral : 21.669 178.015 8364 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.07 % Allowed : 20.20 % Favored : 77.73 % 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 aren not related in a simple way. whole: 0.44 (0.26), residues: 1084 helix: 0.95 (0.23), residues: 503 sheet: 0.14 (0.41), residues: 163 loop : -0.31 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 59 TYR 0.013 0.002 TYR N 20 PHE 0.015 0.002 PHE S 74 TRP 0.020 0.002 TRP B 104 HIS 0.007 0.002 HIS M 12 Details of bonding type rmsd covalent geometry : bond 0.00780 (19733) covalent geometry : angle 0.75600 (28859) hydrogen bonds : bond 0.07553 ( 758) hydrogen bonds : angle 4.30869 ( 1748) metal coordination : bond 0.00111 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6024.28 seconds wall clock time: 103 minutes 28.19 seconds (6208.19 seconds total)