Starting phenix.real_space_refine on Sat Aug 23 11:45:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9j_34569/08_2025/8h9j_34569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9j_34569/08_2025/8h9j_34569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9j_34569/08_2025/8h9j_34569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9j_34569/08_2025/8h9j_34569.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9j_34569/08_2025/8h9j_34569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9j_34569/08_2025/8h9j_34569.cif" } resolution = 3.26 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= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7930 2.51 5 N 1932 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12082 Number of models: 1 Model: "" Number of chains: 19 Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1485 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 30} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Time building chain proxies: 2.22, per 1000 atoms: 0.18 Number of scatterers: 12082 At special positions: 0 Unit cell: (125.56, 87.6, 137.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2157 8.00 N 1932 7.00 C 7930 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: 0.92 Conformation dependent library (CDL) restraints added in 484.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 77.8% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain '6' and resid 1 through 17 removed outlier: 4.121A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 39 Processing helix chain '7' and resid 42 through 73 Processing helix chain '8' and resid 2 through 17 removed outlier: 4.121A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 Processing helix chain '1' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 Processing helix chain '1' and resid 42 through 73 Processing helix chain '2' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 Processing helix chain '3' and resid 2 through 17 removed outlier: 4.121A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 Processing helix chain '4' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 Processing helix chain '5' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 Processing helix chain 'G' and resid 33 through 48 removed outlier: 4.097A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 99 Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.339A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.538A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.966A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.956A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.635A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.631A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.540A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.350A pdb=" N SER N 8 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.677A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 68 through 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.853A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.015A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 137 through 181 Proline residue: N 153 - end of helix removed outlier: 3.815A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 225 Processing helix chain 'P' and resid 4 through 9 removed outlier: 3.578A pdb=" N ASN P 8 " --> pdb=" O SER P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 20 removed outlier: 3.686A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.531A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.372A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 95 removed outlier: 3.502A pdb=" N ARG S 95 " --> pdb=" O ILE S 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 43 Proline residue: T 35 - end of helix Processing helix chain 'T' and resid 44 through 45 No H-bonds generated for 'chain 'T' and resid 44 through 45' Processing helix chain 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 9 through 22 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 removed outlier: 3.579A pdb=" N ASN Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.218A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 3.615A pdb=" N ALA H 31 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.113A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 966 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3673 1.34 - 1.46: 2307 1.46 - 1.57: 6228 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12323 Sorted by residual: bond pdb=" N ARG 5 38 " pdb=" CA ARG 5 38 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.27e-02 6.20e+03 7.24e+00 bond pdb=" N ILE 3 2 " pdb=" CA ILE 3 2 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.30e-02 5.92e+03 6.99e+00 bond pdb=" N ILE 1 2 " pdb=" CA ILE 1 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.90e+00 bond pdb=" N ILE 8 2 " pdb=" CA ILE 8 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.82e+00 bond pdb=" N ILE 2 2 " pdb=" CA ILE 2 2 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.79e+00 ... (remaining 12318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 15788 1.71 - 3.42: 786 3.42 - 5.13: 90 5.13 - 6.84: 19 6.84 - 8.55: 4 Bond angle restraints: 16687 Sorted by residual: angle pdb=" N THR Q 7 " pdb=" CA THR Q 7 " pdb=" C THR Q 7 " ideal model delta sigma weight residual 114.56 106.01 8.55 1.27e+00 6.20e-01 4.53e+01 angle pdb=" C VAL T 5 " pdb=" N GLN T 6 " pdb=" CA GLN T 6 " ideal model delta sigma weight residual 121.31 127.06 -5.75 1.49e+00 4.50e-01 1.49e+01 angle pdb=" N GLN T 6 " pdb=" CA GLN T 6 " pdb=" C GLN T 6 " ideal model delta sigma weight residual 110.35 115.71 -5.36 1.40e+00 5.10e-01 1.47e+01 angle pdb=" C ILE P 9 " pdb=" N TRP P 10 " pdb=" CA TRP P 10 " ideal model delta sigma weight residual 122.79 116.51 6.28 1.78e+00 3.16e-01 1.24e+01 angle pdb=" N PHE N 26 " pdb=" CA PHE N 26 " pdb=" C PHE N 26 " ideal model delta sigma weight residual 109.81 116.94 -7.13 2.21e+00 2.05e-01 1.04e+01 ... (remaining 16682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 6380 14.89 - 29.79: 642 29.79 - 44.68: 187 44.68 - 59.58: 31 59.58 - 74.47: 8 Dihedral angle restraints: 7248 sinusoidal: 2710 harmonic: 4538 Sorted by residual: dihedral pdb=" CA LYS N 120 " pdb=" C LYS N 120 " pdb=" N ILE N 121 " pdb=" CA ILE N 121 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG N 118 " pdb=" C ARG N 118 " pdb=" N SER N 119 " pdb=" CA SER N 119 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET N 57 " pdb=" C MET N 57 " pdb=" N MET N 58 " pdb=" CA MET N 58 " ideal model delta harmonic sigma weight residual 180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 7245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1030 0.035 - 0.070: 632 0.070 - 0.106: 215 0.106 - 0.141: 57 0.141 - 0.176: 37 Chirality restraints: 1971 Sorted by residual: chirality pdb=" CA LEU 8 70 " pdb=" N LEU 8 70 " pdb=" C LEU 8 70 " pdb=" CB LEU 8 70 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA THR N 135 " pdb=" N THR N 135 " pdb=" C THR N 135 " pdb=" CB THR N 135 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA LEU 2 70 " pdb=" N LEU 2 70 " pdb=" C LEU 2 70 " pdb=" CB LEU 2 70 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.29e-01 ... (remaining 1968 not shown) Planarity restraints: 2065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 133 " 0.273 9.50e-02 1.11e+02 1.23e-01 9.23e+00 pdb=" NE ARG G 133 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG G 133 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG G 133 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 133 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS T 12 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C LYS T 12 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS T 12 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU T 13 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 8 38 " 0.183 9.50e-02 1.11e+02 8.22e-02 4.14e+00 pdb=" NE ARG 8 38 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG 8 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 8 38 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG 8 38 " 0.007 2.00e-02 2.50e+03 ... (remaining 2062 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2849 2.77 - 3.30: 13032 3.30 - 3.83: 20715 3.83 - 4.37: 24464 4.37 - 4.90: 41016 Nonbonded interactions: 102076 Sorted by model distance: nonbonded pdb=" OD1 ASN M 136 " pdb=" OG1 THR M 142 " model vdw 2.233 3.040 nonbonded pdb=" O MET N 181 " pdb=" OG1 THR N 189 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR R 50 " pdb=" O GLY R 64 " model vdw 2.256 3.040 nonbonded pdb=" O SER H 88 " pdb=" OG SER H 88 " model vdw 2.265 3.040 nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.278 3.120 ... (remaining 102071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } 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: 11.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.590 Find NCS groups from input model: 0.110 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.010 0.076 12323 Z= 0.473 Angle : 0.846 8.549 16687 Z= 0.497 Chirality : 0.052 0.176 1971 Planarity : 0.006 0.123 2065 Dihedral : 13.196 74.472 4352 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -3.26 (0.18), residues: 1558 helix: -1.78 (0.13), residues: 1113 sheet: -1.57 (0.53), residues: 87 loop : -2.90 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 7 38 TYR 0.024 0.002 TYR T 30 PHE 0.024 0.002 PHE H 45 TRP 0.011 0.002 TRP P 10 HIS 0.007 0.002 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.01047 (12323) covalent geometry : angle 0.84603 (16687) hydrogen bonds : bond 0.13172 ( 960) hydrogen bonds : angle 7.08486 ( 2847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 60 MET cc_start: 0.7499 (mmm) cc_final: 0.7074 (mpp) REVERT: G 77 LEU cc_start: 0.7792 (mp) cc_final: 0.7382 (tt) REVERT: H 32 ASN cc_start: 0.5948 (t0) cc_final: 0.5747 (t0) REVERT: I 13 ILE cc_start: 0.8979 (mm) cc_final: 0.8740 (mm) REVERT: T 36 ARG cc_start: 0.6748 (mpp80) cc_final: 0.6448 (mpp80) REVERT: Q 1 MET cc_start: 0.7790 (mmm) cc_final: 0.7017 (mmm) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1246 time to fit residues: 68.8381 Evaluate side-chains 323 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN G 120 HIS G 163 ASN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS H 85 ASN H 111 ASN H 116 GLN I 42 ASN M 159 ASN N 4 ASN N 46 GLN N 47 GLN N 61 HIS N 123 ASN N 225 ASN P 8 ASN S 50 GLN S 66 GLN Q 32 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.160029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124882 restraints weight = 17610.156| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.49 r_work: 0.3409 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12323 Z= 0.167 Angle : 0.616 9.669 16687 Z= 0.327 Chirality : 0.043 0.169 1971 Planarity : 0.004 0.050 2065 Dihedral : 4.643 59.655 1685 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.71 % Allowed : 15.16 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: -0.48 (0.20), residues: 1558 helix: 0.24 (0.14), residues: 1149 sheet: -1.46 (0.58), residues: 72 loop : -1.64 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 118 TYR 0.018 0.001 TYR K 74 PHE 0.028 0.002 PHE R 79 TRP 0.013 0.002 TRP S 30 HIS 0.008 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00344 (12323) covalent geometry : angle 0.61641 (16687) hydrogen bonds : bond 0.05833 ( 960) hydrogen bonds : angle 4.73574 ( 2847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 335 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 75 MET cc_start: 0.7142 (tpp) cc_final: 0.6192 (mtt) REVERT: G 44 TYR cc_start: 0.8354 (t80) cc_final: 0.8043 (t80) REVERT: H 85 ASN cc_start: 0.7631 (m-40) cc_final: 0.7412 (m110) REVERT: H 102 MET cc_start: 0.5071 (ttm) cc_final: 0.4847 (ttm) REVERT: I 21 LYS cc_start: 0.8269 (tmtt) cc_final: 0.8062 (tptp) REVERT: I 44 LYS cc_start: 0.8780 (mttt) cc_final: 0.8551 (mttm) REVERT: R 29 ILE cc_start: 0.8859 (mp) cc_final: 0.8272 (tp) REVERT: Q 16 MET cc_start: 0.8925 (tmm) cc_final: 0.8721 (tmm) outliers start: 34 outliers final: 16 residues processed: 351 average time/residue: 0.1184 time to fit residues: 59.0879 Evaluate side-chains 310 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 147 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN 4 45 GLN N 4 ASN P 8 ASN S 57 ASN Q 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.158441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.123164 restraints weight = 17897.969| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.54 r_work: 0.3396 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12323 Z= 0.164 Angle : 0.587 8.999 16687 Z= 0.308 Chirality : 0.043 0.180 1971 Planarity : 0.004 0.050 2065 Dihedral : 4.483 59.446 1685 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.27 % Allowed : 18.04 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 0.64 (0.21), residues: 1558 helix: 1.08 (0.15), residues: 1149 sheet: -1.36 (0.57), residues: 72 loop : -1.26 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 159 TYR 0.018 0.001 TYR T 30 PHE 0.034 0.002 PHE 2 69 TRP 0.016 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00357 (12323) covalent geometry : angle 0.58743 (16687) hydrogen bonds : bond 0.05529 ( 960) hydrogen bonds : angle 4.49740 ( 2847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7825 (mm) REVERT: 5 7 LYS cc_start: 0.7681 (mmtp) cc_final: 0.7301 (mmtp) REVERT: G 211 ASN cc_start: 0.8947 (m-40) cc_final: 0.8679 (t0) REVERT: I 44 LYS cc_start: 0.8790 (mttt) cc_final: 0.8565 (mttm) REVERT: N 36 TYR cc_start: 0.8196 (m-10) cc_final: 0.7700 (m-10) REVERT: R 29 ILE cc_start: 0.8794 (mp) cc_final: 0.8302 (tp) REVERT: R 88 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8146 (mtp85) REVERT: Q 16 MET cc_start: 0.8969 (tmm) cc_final: 0.8757 (tmm) outliers start: 41 outliers final: 26 residues processed: 330 average time/residue: 0.1127 time to fit residues: 52.6980 Evaluate side-chains 318 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 3 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 124 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 45 GLN 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Q 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.159477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124223 restraints weight = 17721.433| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.58 r_work: 0.3411 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 12323 Z= 0.152 Angle : 0.575 7.408 16687 Z= 0.301 Chirality : 0.042 0.182 1971 Planarity : 0.004 0.044 2065 Dihedral : 4.442 58.351 1685 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.83 % Allowed : 18.83 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.16 (0.21), residues: 1558 helix: 1.45 (0.15), residues: 1148 sheet: -1.18 (0.57), residues: 72 loop : -1.04 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 159 TYR 0.024 0.001 TYR T 30 PHE 0.026 0.001 PHE R 79 TRP 0.018 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00327 (12323) covalent geometry : angle 0.57539 (16687) hydrogen bonds : bond 0.05263 ( 960) hydrogen bonds : angle 4.38221 ( 2847) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 306 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7813 (mm) REVERT: 4 63 PHE cc_start: 0.7870 (m-10) cc_final: 0.7538 (m-10) REVERT: 5 7 LYS cc_start: 0.7664 (mmtp) cc_final: 0.7317 (mmtp) REVERT: G 46 LEU cc_start: 0.8779 (mt) cc_final: 0.8496 (mm) REVERT: G 147 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8025 (tp30) REVERT: H 102 MET cc_start: 0.5034 (ttm) cc_final: 0.4773 (ttm) REVERT: H 128 ARG cc_start: 0.8569 (mtp85) cc_final: 0.8255 (mtp85) REVERT: I 44 LYS cc_start: 0.8798 (mttt) cc_final: 0.8546 (mttm) REVERT: K 51 TYR cc_start: 0.8967 (t80) cc_final: 0.8740 (t80) REVERT: K 87 GLU cc_start: 0.7736 (mp0) cc_final: 0.7503 (mp0) REVERT: N 36 TYR cc_start: 0.8170 (m-10) cc_final: 0.7652 (m-10) REVERT: P 14 LYS cc_start: 0.8247 (tttm) cc_final: 0.7884 (mtpt) REVERT: R 28 TRP cc_start: 0.8446 (t60) cc_final: 0.8163 (t60) REVERT: R 29 ILE cc_start: 0.8794 (mp) cc_final: 0.8255 (tp) REVERT: R 88 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8149 (mtp85) REVERT: T 30 TYR cc_start: 0.6461 (t80) cc_final: 0.6243 (t80) outliers start: 48 outliers final: 32 residues processed: 324 average time/residue: 0.1191 time to fit residues: 54.5605 Evaluate side-chains 322 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 65 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 45 GLN Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 31 SER Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 45 GLN Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 71 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 3 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 109 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN N 4 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN S 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.160136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125370 restraints weight = 17756.847| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.55 r_work: 0.3421 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12323 Z= 0.144 Angle : 0.565 7.555 16687 Z= 0.296 Chirality : 0.041 0.183 1971 Planarity : 0.004 0.045 2065 Dihedral : 4.373 55.902 1685 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.43 % Allowed : 20.91 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.49 (0.21), residues: 1558 helix: 1.71 (0.15), residues: 1136 sheet: -1.02 (0.58), residues: 72 loop : -0.90 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 118 TYR 0.021 0.001 TYR T 30 PHE 0.025 0.001 PHE R 79 TRP 0.011 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00298 (12323) covalent geometry : angle 0.56488 (16687) hydrogen bonds : bond 0.05090 ( 960) hydrogen bonds : angle 4.29500 ( 2847) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 301 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7773 (mm) REVERT: 7 75 MET cc_start: 0.7281 (tpp) cc_final: 0.6057 (mtt) REVERT: 4 63 PHE cc_start: 0.7874 (m-10) cc_final: 0.7551 (m-10) REVERT: 5 7 LYS cc_start: 0.7656 (mmtp) cc_final: 0.7329 (mmtp) REVERT: G 37 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6773 (mt-10) REVERT: G 46 LEU cc_start: 0.8707 (mt) cc_final: 0.8448 (mm) REVERT: G 147 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8039 (tp30) REVERT: H 102 MET cc_start: 0.5053 (ttm) cc_final: 0.4823 (ttm) REVERT: H 128 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8253 (mtp85) REVERT: I 44 LYS cc_start: 0.8809 (mttt) cc_final: 0.8565 (mttm) REVERT: K 51 TYR cc_start: 0.8975 (t80) cc_final: 0.8747 (t80) REVERT: K 87 GLU cc_start: 0.7730 (mp0) cc_final: 0.7490 (mp0) REVERT: N 36 TYR cc_start: 0.8169 (m-10) cc_final: 0.7694 (m-10) REVERT: P 14 LYS cc_start: 0.8271 (tttm) cc_final: 0.7927 (mtpt) REVERT: R 29 ILE cc_start: 0.8771 (mp) cc_final: 0.8336 (tp) REVERT: S 53 LYS cc_start: 0.7916 (pttt) cc_final: 0.7709 (mmtt) outliers start: 43 outliers final: 31 residues processed: 323 average time/residue: 0.1089 time to fit residues: 49.3360 Evaluate side-chains 324 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 54 PHE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 111 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN 8 45 GLN 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN P 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.158886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123819 restraints weight = 17636.015| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.47 r_work: 0.3397 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12323 Z= 0.161 Angle : 0.587 7.759 16687 Z= 0.304 Chirality : 0.042 0.203 1971 Planarity : 0.004 0.046 2065 Dihedral : 4.381 56.257 1685 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.83 % Allowed : 21.47 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.58 (0.21), residues: 1558 helix: 1.75 (0.15), residues: 1142 sheet: -0.75 (0.55), residues: 80 loop : -0.90 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 118 TYR 0.029 0.001 TYR T 30 PHE 0.025 0.001 PHE R 79 TRP 0.012 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00354 (12323) covalent geometry : angle 0.58653 (16687) hydrogen bonds : bond 0.05113 ( 960) hydrogen bonds : angle 4.29424 ( 2847) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7819 (mm) REVERT: 4 63 PHE cc_start: 0.7911 (m-10) cc_final: 0.7582 (m-10) REVERT: 5 7 LYS cc_start: 0.7657 (mmtp) cc_final: 0.7358 (mmtp) REVERT: G 37 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6815 (mt-10) REVERT: G 46 LEU cc_start: 0.8683 (mt) cc_final: 0.8421 (mm) REVERT: G 147 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8045 (tp30) REVERT: H 16 MET cc_start: 0.5100 (ttm) cc_final: 0.4887 (tpt) REVERT: H 102 MET cc_start: 0.4964 (ttm) cc_final: 0.4695 (ttm) REVERT: H 128 ARG cc_start: 0.8587 (mtp85) cc_final: 0.8230 (mtp85) REVERT: I 44 LYS cc_start: 0.8822 (mttt) cc_final: 0.8567 (mttm) REVERT: K 51 TYR cc_start: 0.8988 (t80) cc_final: 0.8744 (t80) REVERT: K 87 GLU cc_start: 0.7755 (mp0) cc_final: 0.7511 (mp0) REVERT: N 36 TYR cc_start: 0.8182 (m-10) cc_final: 0.7800 (m-10) REVERT: N 159 ARG cc_start: 0.9133 (ttm110) cc_final: 0.8919 (ttm170) REVERT: P 14 LYS cc_start: 0.8239 (tttm) cc_final: 0.7870 (mtpt) REVERT: R 69 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7130 (mp) REVERT: R 88 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8219 (mtp85) REVERT: S 31 TYR cc_start: 0.8392 (t80) cc_final: 0.8110 (t80) REVERT: S 53 LYS cc_start: 0.7912 (pttt) cc_final: 0.7685 (mmtt) outliers start: 48 outliers final: 35 residues processed: 320 average time/residue: 0.1156 time to fit residues: 51.8909 Evaluate side-chains 328 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 66 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN N 4 ASN P 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124154 restraints weight = 17737.366| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.49 r_work: 0.3403 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12323 Z= 0.151 Angle : 0.592 10.495 16687 Z= 0.302 Chirality : 0.042 0.210 1971 Planarity : 0.004 0.044 2065 Dihedral : 4.342 54.968 1685 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.67 % Allowed : 22.35 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.77 (0.21), residues: 1558 helix: 1.90 (0.15), residues: 1130 sheet: -0.73 (0.55), residues: 80 loop : -0.74 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 118 TYR 0.036 0.001 TYR T 30 PHE 0.026 0.001 PHE R 79 TRP 0.026 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00324 (12323) covalent geometry : angle 0.59151 (16687) hydrogen bonds : bond 0.05019 ( 960) hydrogen bonds : angle 4.25522 ( 2847) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7787 (mm) REVERT: 1 39 ASN cc_start: 0.7485 (t0) cc_final: 0.7135 (p0) REVERT: 4 63 PHE cc_start: 0.7890 (m-10) cc_final: 0.7600 (m-10) REVERT: 5 7 LYS cc_start: 0.7642 (mmtp) cc_final: 0.7384 (mmtp) REVERT: G 37 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6858 (mt-10) REVERT: G 46 LEU cc_start: 0.8660 (mt) cc_final: 0.8369 (mm) REVERT: G 147 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8036 (tp30) REVERT: H 122 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7846 (p) REVERT: H 128 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8087 (mtp85) REVERT: I 44 LYS cc_start: 0.8811 (mttt) cc_final: 0.8573 (mttm) REVERT: K 51 TYR cc_start: 0.8968 (t80) cc_final: 0.8717 (t80) REVERT: K 87 GLU cc_start: 0.7807 (mp0) cc_final: 0.7570 (mp0) REVERT: N 36 TYR cc_start: 0.8171 (m-10) cc_final: 0.7828 (m-10) REVERT: N 147 ILE cc_start: 0.8872 (tp) cc_final: 0.8583 (tp) REVERT: P 14 LYS cc_start: 0.8275 (tttm) cc_final: 0.7905 (mtpt) REVERT: R 28 TRP cc_start: 0.8470 (t60) cc_final: 0.8151 (t60) REVERT: R 88 ARG cc_start: 0.8476 (mtp85) cc_final: 0.8195 (mtp85) REVERT: S 31 TYR cc_start: 0.8400 (t80) cc_final: 0.8158 (t80) REVERT: S 53 LYS cc_start: 0.7950 (pttt) cc_final: 0.7706 (mmtt) REVERT: T 13 LEU cc_start: 0.6563 (mm) cc_final: 0.6312 (mm) outliers start: 46 outliers final: 35 residues processed: 322 average time/residue: 0.1079 time to fit residues: 49.3748 Evaluate side-chains 324 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 287 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 45 GLN Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 2 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN K 23 GLN N 4 ASN P 8 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124755 restraints weight = 17612.847| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.59 r_work: 0.3415 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12323 Z= 0.144 Angle : 0.598 9.806 16687 Z= 0.304 Chirality : 0.042 0.218 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.303 53.188 1685 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.27 % Allowed : 23.46 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.84 (0.21), residues: 1558 helix: 1.95 (0.15), residues: 1129 sheet: -0.66 (0.56), residues: 80 loop : -0.70 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 36 TYR 0.031 0.001 TYR T 30 PHE 0.025 0.001 PHE R 79 TRP 0.018 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00306 (12323) covalent geometry : angle 0.59784 (16687) hydrogen bonds : bond 0.04935 ( 960) hydrogen bonds : angle 4.23772 ( 2847) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7800 (mm) REVERT: 1 39 ASN cc_start: 0.7432 (t0) cc_final: 0.7115 (p0) REVERT: 1 60 MET cc_start: 0.7149 (mmt) cc_final: 0.6588 (mmt) REVERT: 4 63 PHE cc_start: 0.7895 (m-10) cc_final: 0.7652 (m-80) REVERT: 5 7 LYS cc_start: 0.7649 (mmtp) cc_final: 0.7382 (mmtp) REVERT: G 46 LEU cc_start: 0.8618 (mt) cc_final: 0.8328 (mm) REVERT: G 52 TYR cc_start: 0.6969 (m-80) cc_final: 0.6640 (m-80) REVERT: G 147 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8018 (tp30) REVERT: G 189 SER cc_start: 0.7323 (t) cc_final: 0.7052 (p) REVERT: H 96 GLU cc_start: 0.7725 (tp30) cc_final: 0.7476 (tp30) REVERT: H 102 MET cc_start: 0.5071 (ttm) cc_final: 0.4824 (ttm) REVERT: H 122 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7910 (p) REVERT: H 128 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8088 (mtp85) REVERT: I 44 LYS cc_start: 0.8809 (mttt) cc_final: 0.8577 (mttm) REVERT: K 51 TYR cc_start: 0.8960 (t80) cc_final: 0.8726 (t80) REVERT: K 87 GLU cc_start: 0.7778 (mp0) cc_final: 0.7560 (mp0) REVERT: N 35 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7929 (ptpt) REVERT: N 36 TYR cc_start: 0.8170 (m-10) cc_final: 0.7838 (m-10) REVERT: N 147 ILE cc_start: 0.8878 (tp) cc_final: 0.8594 (tp) REVERT: P 14 LYS cc_start: 0.8299 (tttm) cc_final: 0.7944 (mtpt) REVERT: R 82 LYS cc_start: 0.8998 (mtmm) cc_final: 0.8047 (mptt) REVERT: R 88 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8180 (mtp85) REVERT: S 31 TYR cc_start: 0.8387 (t80) cc_final: 0.8186 (t80) REVERT: S 53 LYS cc_start: 0.8014 (pttt) cc_final: 0.7769 (mmtt) REVERT: T 13 LEU cc_start: 0.6587 (mm) cc_final: 0.6353 (mm) outliers start: 41 outliers final: 32 residues processed: 321 average time/residue: 0.1104 time to fit residues: 49.9419 Evaluate side-chains 321 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 54 PHE Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 45 GLN Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 38 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.161475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126617 restraints weight = 17629.803| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.54 r_work: 0.3441 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12323 Z= 0.135 Angle : 0.595 9.533 16687 Z= 0.302 Chirality : 0.041 0.230 1971 Planarity : 0.004 0.044 2065 Dihedral : 4.242 49.136 1685 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.03 % Allowed : 23.62 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.94 (0.21), residues: 1558 helix: 2.02 (0.15), residues: 1129 sheet: -0.67 (0.56), residues: 78 loop : -0.62 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 118 TYR 0.026 0.001 TYR T 30 PHE 0.025 0.001 PHE R 79 TRP 0.029 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00282 (12323) covalent geometry : angle 0.59514 (16687) hydrogen bonds : bond 0.04794 ( 960) hydrogen bonds : angle 4.20344 ( 2847) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 296 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7817 (mm) REVERT: 1 39 ASN cc_start: 0.7292 (t0) cc_final: 0.7087 (p0) REVERT: 4 63 PHE cc_start: 0.7816 (m-10) cc_final: 0.7583 (m-10) REVERT: 5 7 LYS cc_start: 0.7599 (mmtp) cc_final: 0.7375 (mmtp) REVERT: G 46 LEU cc_start: 0.8583 (mt) cc_final: 0.8297 (mm) REVERT: G 52 TYR cc_start: 0.6956 (m-80) cc_final: 0.6565 (m-80) REVERT: G 133 ARG cc_start: 0.8680 (ttt-90) cc_final: 0.7735 (tpp80) REVERT: G 147 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7952 (tp30) REVERT: G 189 SER cc_start: 0.7322 (t) cc_final: 0.7085 (p) REVERT: H 96 GLU cc_start: 0.7748 (tp30) cc_final: 0.7503 (tp30) REVERT: H 102 MET cc_start: 0.5071 (ttm) cc_final: 0.4839 (ttm) REVERT: H 109 LYS cc_start: 0.8321 (mttp) cc_final: 0.8069 (mttm) REVERT: H 122 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7917 (p) REVERT: H 128 ARG cc_start: 0.8545 (mtp85) cc_final: 0.8059 (mtp85) REVERT: I 44 LYS cc_start: 0.8794 (mttt) cc_final: 0.8580 (mttm) REVERT: K 26 TYR cc_start: 0.8542 (t80) cc_final: 0.8272 (t80) REVERT: K 51 TYR cc_start: 0.8977 (t80) cc_final: 0.8752 (t80) REVERT: N 35 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7934 (ptpt) REVERT: N 36 TYR cc_start: 0.8134 (m-10) cc_final: 0.7841 (m-10) REVERT: N 147 ILE cc_start: 0.8860 (tp) cc_final: 0.8577 (tp) REVERT: P 14 LYS cc_start: 0.8313 (tttm) cc_final: 0.7965 (mtpt) REVERT: R 82 LYS cc_start: 0.8988 (mtmm) cc_final: 0.8069 (mptt) REVERT: R 88 ARG cc_start: 0.8431 (mtp85) cc_final: 0.8176 (mtp85) REVERT: S 53 LYS cc_start: 0.8002 (pttt) cc_final: 0.7754 (mmtt) REVERT: T 13 LEU cc_start: 0.6599 (mm) cc_final: 0.6376 (mm) outliers start: 38 outliers final: 31 residues processed: 315 average time/residue: 0.1116 time to fit residues: 49.4706 Evaluate side-chains 322 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 45 GLN Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 chunk 82 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.161306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127472 restraints weight = 17572.020| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.43 r_work: 0.3449 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12323 Z= 0.142 Angle : 0.607 9.962 16687 Z= 0.306 Chirality : 0.042 0.240 1971 Planarity : 0.004 0.048 2065 Dihedral : 4.224 47.256 1685 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.71 % Allowed : 24.34 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.93 (0.21), residues: 1558 helix: 2.00 (0.15), residues: 1129 sheet: -0.69 (0.56), residues: 78 loop : -0.58 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 159 TYR 0.013 0.001 TYR G 44 PHE 0.024 0.001 PHE R 79 TRP 0.022 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00306 (12323) covalent geometry : angle 0.60672 (16687) hydrogen bonds : bond 0.04827 ( 960) hydrogen bonds : angle 4.21390 ( 2847) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8140 (mm) cc_final: 0.7860 (mm) REVERT: 7 16 VAL cc_start: 0.7436 (p) cc_final: 0.7224 (p) REVERT: 5 7 LYS cc_start: 0.7626 (mmtp) cc_final: 0.7405 (mmtp) REVERT: G 46 LEU cc_start: 0.8594 (mt) cc_final: 0.8322 (mm) REVERT: G 52 TYR cc_start: 0.6932 (m-80) cc_final: 0.6628 (m-80) REVERT: G 133 ARG cc_start: 0.8689 (ttt-90) cc_final: 0.7749 (tpp80) REVERT: G 147 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7970 (tp30) REVERT: G 189 SER cc_start: 0.7330 (t) cc_final: 0.7098 (p) REVERT: H 96 GLU cc_start: 0.7717 (tp30) cc_final: 0.7495 (tp30) REVERT: H 102 MET cc_start: 0.5140 (ttm) cc_final: 0.4898 (ttm) REVERT: H 122 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7943 (p) REVERT: H 128 ARG cc_start: 0.8602 (mtp85) cc_final: 0.8166 (mtp85) REVERT: I 44 LYS cc_start: 0.8832 (mttt) cc_final: 0.8621 (mttm) REVERT: K 26 TYR cc_start: 0.8569 (t80) cc_final: 0.8314 (t80) REVERT: K 51 TYR cc_start: 0.8978 (t80) cc_final: 0.8725 (t80) REVERT: K 87 GLU cc_start: 0.7784 (mp0) cc_final: 0.7411 (mp0) REVERT: M 145 ASP cc_start: 0.8646 (t0) cc_final: 0.8431 (t0) REVERT: N 35 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8015 (ptpt) REVERT: N 36 TYR cc_start: 0.8124 (m-10) cc_final: 0.7849 (m-10) REVERT: N 147 ILE cc_start: 0.8881 (tp) cc_final: 0.8596 (tp) REVERT: P 14 LYS cc_start: 0.8381 (tttm) cc_final: 0.8034 (mtpt) REVERT: R 82 LYS cc_start: 0.8994 (mtmm) cc_final: 0.8097 (mptt) REVERT: R 88 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8138 (mtp85) REVERT: S 53 LYS cc_start: 0.8016 (pttt) cc_final: 0.7746 (mmtt) outliers start: 34 outliers final: 32 residues processed: 310 average time/residue: 0.1108 time to fit residues: 48.4489 Evaluate side-chains 317 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 2 residue 65 LEU Chi-restraints excluded: chain 3 residue 25 ILE Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 45 GLN Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 140 MET Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 45 GLN 3 45 GLN 4 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.157055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122290 restraints weight = 17710.227| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.31 r_work: 0.3376 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12323 Z= 0.202 Angle : 0.656 9.767 16687 Z= 0.335 Chirality : 0.045 0.246 1971 Planarity : 0.004 0.053 2065 Dihedral : 4.368 51.998 1685 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.03 % Allowed : 24.58 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % 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: 1.74 (0.21), residues: 1558 helix: 1.88 (0.15), residues: 1129 sheet: -1.08 (0.53), residues: 85 loop : -0.62 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 159 TYR 0.031 0.002 TYR T 30 PHE 0.026 0.002 PHE R 79 TRP 0.032 0.002 TRP R 28 HIS 0.006 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00466 (12323) covalent geometry : angle 0.65605 (16687) hydrogen bonds : bond 0.05300 ( 960) hydrogen bonds : angle 4.33869 ( 2847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3391.49 seconds wall clock time: 58 minutes 54.65 seconds (3534.65 seconds total)