Starting phenix.real_space_refine on Wed May 14 13:56:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9j_34569/05_2025/8h9j_34569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9j_34569/05_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_34569/05_2025/8h9j_34569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9j_34569/05_2025/8h9j_34569.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9j_34569/05_2025/8h9j_34569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9j_34569/05_2025/8h9j_34569.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.11, per 1000 atoms: 0.75 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: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.17 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: 3.65 Time building geometry restraints manager: 3.78 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: 18.840 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 31.570 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.640 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.002 TRP P 10 HIS 0.007 0.002 HIS N 127 PHE 0.024 0.002 PHE H 45 TYR 0.024 0.002 TYR T 30 ARG 0.004 0.001 ARG 7 38 Details of bonding type rmsd hydrogen bonds : bond 0.13172 ( 960) hydrogen bonds : angle 7.08486 ( 2847) covalent geometry : bond 0.01047 (12323) covalent geometry : angle 0.84603 (16687) *********************** 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 : 1.222 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: 0.7072 (mpp) REVERT: G 77 LEU cc_start: 0.7792 (mp) cc_final: 0.7385 (tt) REVERT: I 13 ILE cc_start: 0.8979 (mm) cc_final: 0.8739 (mm) REVERT: T 36 ARG cc_start: 0.6748 (mpp80) cc_final: 0.6447 (mpp80) REVERT: Q 1 MET cc_start: 0.7790 (mmm) cc_final: 0.7018 (mmm) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.2596 time to fit residues: 142.2072 Evaluate side-chains 321 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 H 66 HIS H 85 ASN H 111 ASN H 116 GLN I 42 ASN K 23 GLN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.158128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122927 restraints weight = 17712.369| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.51 r_work: 0.3397 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2185 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= 0.171 Angle : 0.617 9.591 16687 Z= 0.327 Chirality : 0.043 0.173 1971 Planarity : 0.004 0.051 2065 Dihedral : 4.652 60.434 1685 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.55 % Allowed : 15.72 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1558 helix: 0.15 (0.14), residues: 1148 sheet: -1.42 (0.58), residues: 72 loop : -1.72 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 30 HIS 0.008 0.001 HIS N 127 PHE 0.027 0.002 PHE R 79 TYR 0.018 0.001 TYR K 74 ARG 0.008 0.001 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.06026 ( 960) hydrogen bonds : angle 4.77838 ( 2847) covalent geometry : bond 0.00349 (12323) covalent geometry : angle 0.61715 (16687) *********************** 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 367 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 335 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 75 MET cc_start: 0.7171 (tpp) cc_final: 0.6209 (mtt) REVERT: G 44 TYR cc_start: 0.8383 (t80) cc_final: 0.8122 (t80) REVERT: H 85 ASN cc_start: 0.7652 (m-40) cc_final: 0.7418 (m110) REVERT: H 102 MET cc_start: 0.5060 (ttm) cc_final: 0.4831 (ttm) REVERT: K 26 TYR cc_start: 0.8453 (t80) cc_final: 0.8250 (t80) REVERT: R 29 ILE cc_start: 0.8856 (mp) cc_final: 0.8303 (tp) REVERT: Q 16 MET cc_start: 0.8946 (tmm) cc_final: 0.8715 (tmm) outliers start: 32 outliers final: 17 residues processed: 350 average time/residue: 0.2453 time to fit residues: 120.5375 Evaluate side-chains 312 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 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 N residue 4 ASN Chi-restraints excluded: chain T residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN M 159 ASN P 8 ASN S 57 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 = 0.3972 r_free = 0.3972 target = 0.158827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123756 restraints weight = 17852.493| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.50 r_work: 0.3406 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12323 Z= 0.156 Angle : 0.587 8.886 16687 Z= 0.307 Chirality : 0.042 0.176 1971 Planarity : 0.004 0.051 2065 Dihedral : 4.507 58.898 1685 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.95 % Allowed : 18.44 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1558 helix: 1.03 (0.15), residues: 1149 sheet: -1.33 (0.57), residues: 72 loop : -1.32 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.034 0.002 PHE 2 69 TYR 0.017 0.001 TYR T 30 ARG 0.009 0.001 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.05504 ( 960) hydrogen bonds : angle 4.51491 ( 2847) covalent geometry : bond 0.00325 (12323) covalent geometry : angle 0.58695 (16687) *********************** 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 356 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 319 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 7 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7312 (mmtp) REVERT: G 44 TYR cc_start: 0.8405 (t80) cc_final: 0.8173 (t80) REVERT: G 211 ASN cc_start: 0.8938 (m-40) cc_final: 0.8645 (t0) REVERT: N 36 TYR cc_start: 0.8177 (m-10) cc_final: 0.7587 (m-10) REVERT: R 29 ILE cc_start: 0.8801 (mp) cc_final: 0.8312 (tp) REVERT: R 88 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8155 (mtp85) REVERT: Q 16 MET cc_start: 0.8938 (tmm) cc_final: 0.8735 (tmm) outliers start: 37 outliers final: 24 residues processed: 334 average time/residue: 0.2517 time to fit residues: 117.1591 Evaluate side-chains 321 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 297 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 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 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 14 ILE Chi-restraints excluded: chain N residue 151 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 33 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 147 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 45 GLN 8 45 GLN 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN N 4 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Q 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124125 restraints weight = 17657.572| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.51 r_work: 0.3407 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12323 Z= 0.154 Angle : 0.569 7.563 16687 Z= 0.300 Chirality : 0.042 0.180 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.472 58.264 1685 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.91 % Allowed : 18.28 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1558 helix: 1.44 (0.15), residues: 1148 sheet: -1.13 (0.58), residues: 72 loop : -1.06 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.001 PHE R 79 TYR 0.024 0.001 TYR T 30 ARG 0.007 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.05266 ( 960) hydrogen bonds : angle 4.37662 ( 2847) covalent geometry : bond 0.00330 (12323) covalent geometry : angle 0.56934 (16687) *********************** 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 356 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 307 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7816 (mm) REVERT: 4 63 PHE cc_start: 0.7879 (m-10) cc_final: 0.7547 (m-10) REVERT: 5 7 LYS cc_start: 0.7688 (mmtp) cc_final: 0.7342 (mmtp) REVERT: G 44 TYR cc_start: 0.8245 (t80) cc_final: 0.7906 (t80) REVERT: G 147 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8028 (tp30) REVERT: G 211 ASN cc_start: 0.8894 (m-40) cc_final: 0.8578 (t0) REVERT: H 128 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8324 (mtp85) REVERT: K 87 GLU cc_start: 0.7750 (mp0) cc_final: 0.7433 (mp0) REVERT: N 36 TYR cc_start: 0.8184 (m-10) cc_final: 0.7674 (m-10) REVERT: P 7 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7496 (mtmm) REVERT: P 14 LYS cc_start: 0.8251 (tttm) cc_final: 0.7891 (mtpt) REVERT: R 29 ILE cc_start: 0.8801 (mp) cc_final: 0.8348 (tp) REVERT: R 88 ARG cc_start: 0.8385 (mtp85) cc_final: 0.8154 (mtp85) REVERT: S 53 LYS cc_start: 0.8159 (pttt) cc_final: 0.7941 (mmtt) REVERT: T 30 TYR cc_start: 0.6500 (t80) cc_final: 0.6286 (t80) outliers start: 49 outliers final: 32 residues processed: 328 average time/residue: 0.2675 time to fit residues: 124.5834 Evaluate side-chains 324 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 45 GLN Chi-restraints excluded: chain 7 residue 54 PHE 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 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 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 K residue 25 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** I 42 ASN N 4 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.159908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124441 restraints weight = 17722.130| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.66 r_work: 0.3413 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12323 Z= 0.143 Angle : 0.568 7.718 16687 Z= 0.296 Chirality : 0.041 0.184 1971 Planarity : 0.004 0.045 2065 Dihedral : 4.415 56.078 1685 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.15 % Allowed : 19.31 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.21), residues: 1558 helix: 1.65 (0.15), residues: 1147 sheet: -0.97 (0.58), residues: 72 loop : -0.97 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.027 0.001 PHE R 79 TYR 0.020 0.001 TYR T 30 ARG 0.009 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 960) hydrogen bonds : angle 4.29520 ( 2847) covalent geometry : bond 0.00297 (12323) covalent geometry : angle 0.56814 (16687) *********************** 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 349 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7797 (mm) REVERT: 5 7 LYS cc_start: 0.7680 (mmtp) cc_final: 0.7344 (mmtp) REVERT: G 44 TYR cc_start: 0.8163 (t80) cc_final: 0.7804 (t80) REVERT: G 147 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8037 (tp30) REVERT: G 211 ASN cc_start: 0.8886 (m-40) cc_final: 0.8626 (t0) REVERT: H 128 ARG cc_start: 0.8525 (mtp85) cc_final: 0.8251 (mtp85) REVERT: K 51 TYR cc_start: 0.8979 (t80) cc_final: 0.8758 (t80) REVERT: K 87 GLU cc_start: 0.7720 (mp0) cc_final: 0.7486 (mp0) REVERT: N 36 TYR cc_start: 0.8174 (m-10) cc_final: 0.7699 (m-10) REVERT: P 14 LYS cc_start: 0.8266 (tttm) cc_final: 0.7905 (mtpt) REVERT: R 28 TRP cc_start: 0.8466 (t60) cc_final: 0.8183 (t60) REVERT: R 29 ILE cc_start: 0.8783 (mp) cc_final: 0.8257 (tp) outliers start: 52 outliers final: 33 residues processed: 319 average time/residue: 0.2543 time to fit residues: 112.6335 Evaluate side-chains 324 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 54 PHE Chi-restraints excluded: chain 7 residue 72 LEU 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 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 131 VAL 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 K residue 25 LEU 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 171 MET 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 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 23 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** I 42 ASN ** N 225 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 = 0.3979 r_free = 0.3979 target = 0.159336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.124460 restraints weight = 17876.507| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.54 r_work: 0.3411 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12323 Z= 0.152 Angle : 0.573 7.606 16687 Z= 0.298 Chirality : 0.042 0.195 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.391 55.347 1685 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.83 % Allowed : 20.67 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1558 helix: 1.81 (0.15), residues: 1137 sheet: -0.76 (0.56), residues: 80 loop : -0.85 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.001 PHE R 79 TYR 0.028 0.001 TYR T 30 ARG 0.003 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 960) hydrogen bonds : angle 4.27624 ( 2847) covalent geometry : bond 0.00332 (12323) covalent geometry : angle 0.57305 (16687) *********************** 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 : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7790 (mm) REVERT: 1 65 LEU cc_start: 0.8393 (mt) cc_final: 0.8192 (mt) REVERT: 4 63 PHE cc_start: 0.7879 (m-10) cc_final: 0.7572 (m-10) REVERT: 5 7 LYS cc_start: 0.7671 (mmtp) cc_final: 0.7374 (mmtp) REVERT: G 44 TYR cc_start: 0.8155 (t80) cc_final: 0.7801 (t80) REVERT: G 46 LEU cc_start: 0.8709 (mt) cc_final: 0.8380 (mm) REVERT: G 147 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8004 (tp30) REVERT: G 211 ASN cc_start: 0.8878 (m-40) cc_final: 0.8612 (m-40) REVERT: H 128 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8294 (mtp85) REVERT: K 51 TYR cc_start: 0.8981 (t80) cc_final: 0.8746 (t80) REVERT: K 87 GLU cc_start: 0.7720 (mp0) cc_final: 0.7479 (mp0) REVERT: N 36 TYR cc_start: 0.8189 (m-10) cc_final: 0.7717 (m-10) REVERT: N 159 ARG cc_start: 0.9123 (ttm110) cc_final: 0.8921 (ttm170) REVERT: P 14 LYS cc_start: 0.8270 (tttm) cc_final: 0.7913 (mtpt) REVERT: R 29 ILE cc_start: 0.8742 (mp) cc_final: 0.8279 (tp) REVERT: R 69 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7100 (mp) REVERT: S 31 TYR cc_start: 0.8419 (t80) cc_final: 0.8117 (t80) REVERT: S 53 LYS cc_start: 0.8097 (pttt) cc_final: 0.7881 (mmtt) outliers start: 48 outliers final: 35 residues processed: 318 average time/residue: 0.2621 time to fit residues: 116.6026 Evaluate side-chains 323 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 27 THR 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 51 ILE Chi-restraints excluded: chain 2 residue 4 THR 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 131 VAL 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 N residue 206 VAL 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 68 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 5 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN N 4 ASN R 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.154063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118571 restraints weight = 18085.741| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.59 r_work: 0.3333 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12323 Z= 0.232 Angle : 0.660 10.238 16687 Z= 0.342 Chirality : 0.045 0.203 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.606 63.045 1685 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.31 % Allowed : 20.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.21), residues: 1558 helix: 1.62 (0.15), residues: 1137 sheet: -0.85 (0.56), residues: 80 loop : -0.80 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.027 0.002 PHE R 79 TYR 0.041 0.002 TYR T 30 ARG 0.010 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.05672 ( 960) hydrogen bonds : angle 4.45995 ( 2847) covalent geometry : bond 0.00542 (12323) covalent geometry : angle 0.65958 (16687) *********************** 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 353 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7833 (mm) REVERT: 5 7 LYS cc_start: 0.7729 (mmtp) cc_final: 0.7429 (mmtp) REVERT: G 130 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: G 147 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8004 (tp30) REVERT: G 189 SER cc_start: 0.7487 (t) cc_final: 0.7189 (p) REVERT: H 122 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7837 (p) REVERT: H 128 ARG cc_start: 0.8630 (mtp85) cc_final: 0.8131 (mtp85) REVERT: K 87 GLU cc_start: 0.7806 (mp0) cc_final: 0.7579 (mp0) REVERT: N 36 TYR cc_start: 0.8238 (m-10) cc_final: 0.7747 (m-10) REVERT: P 14 LYS cc_start: 0.8248 (tttm) cc_final: 0.7956 (tttm) REVERT: R 28 TRP cc_start: 0.8489 (t60) cc_final: 0.8241 (t60) REVERT: R 69 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7061 (mp) REVERT: S 31 TYR cc_start: 0.8456 (t80) cc_final: 0.8166 (t80) REVERT: S 53 LYS cc_start: 0.8235 (pttt) cc_final: 0.7981 (mmtt) outliers start: 54 outliers final: 37 residues processed: 331 average time/residue: 0.2587 time to fit residues: 120.0226 Evaluate side-chains 331 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 27 THR 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 51 ILE Chi-restraints excluded: chain 2 residue 4 THR 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 51 ILE 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 130 GLU Chi-restraints excluded: chain G residue 131 VAL 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 124 optimal weight: 0.7980 chunk 144 optimal weight: 0.1980 chunk 130 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 45 GLN 5 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3970 r_free = 0.3970 target = 0.158636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.123798 restraints weight = 17930.385| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.61 r_work: 0.3403 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12323 Z= 0.141 Angle : 0.599 9.633 16687 Z= 0.308 Chirality : 0.042 0.212 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.471 58.945 1685 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.51 % Allowed : 22.75 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.21), residues: 1558 helix: 1.87 (0.15), residues: 1137 sheet: -0.74 (0.56), residues: 80 loop : -0.69 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.031 0.001 TYR T 30 ARG 0.005 0.000 ARG T 36 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 960) hydrogen bonds : angle 4.27760 ( 2847) covalent geometry : bond 0.00296 (12323) covalent geometry : angle 0.59880 (16687) *********************** 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 339 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 295 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7798 (mm) REVERT: 4 63 PHE cc_start: 0.7919 (m-10) cc_final: 0.7664 (m-80) REVERT: 5 7 LYS cc_start: 0.7701 (mmtp) cc_final: 0.7436 (mmtp) REVERT: G 46 LEU cc_start: 0.8698 (mt) cc_final: 0.8388 (mm) REVERT: G 147 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8020 (tp30) REVERT: G 189 SER cc_start: 0.7371 (t) cc_final: 0.7140 (p) REVERT: H 109 LYS cc_start: 0.8360 (mttm) cc_final: 0.8153 (mttm) REVERT: H 122 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7914 (p) REVERT: H 128 ARG cc_start: 0.8588 (mtp85) cc_final: 0.8119 (mtp85) REVERT: K 87 GLU cc_start: 0.7762 (mp0) cc_final: 0.7557 (mp0) REVERT: N 36 TYR cc_start: 0.8179 (m-10) cc_final: 0.7723 (m-10) REVERT: N 147 ILE cc_start: 0.8888 (tp) cc_final: 0.8612 (tp) REVERT: N 159 ARG cc_start: 0.9080 (ttm110) cc_final: 0.8850 (ttm170) REVERT: P 14 LYS cc_start: 0.8285 (tttm) cc_final: 0.7931 (mtpt) REVERT: R 28 TRP cc_start: 0.8512 (t60) cc_final: 0.8245 (t60) REVERT: S 31 TYR cc_start: 0.8449 (t80) cc_final: 0.8207 (t80) REVERT: S 53 LYS cc_start: 0.8208 (pttt) cc_final: 0.7965 (mmtt) outliers start: 44 outliers final: 35 residues processed: 321 average time/residue: 0.2536 time to fit residues: 113.4097 Evaluate side-chains 322 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 45 GLN 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 4 THR 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 51 ILE 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 45 GLN 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 131 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 182 ASN 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 171 MET Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 119 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.158743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124495 restraints weight = 17750.564| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.45 r_work: 0.3406 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12323 Z= 0.148 Angle : 0.603 9.675 16687 Z= 0.309 Chirality : 0.042 0.238 1971 Planarity : 0.004 0.048 2065 Dihedral : 4.445 58.104 1685 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.11 % Allowed : 23.14 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.21), residues: 1558 helix: 1.91 (0.15), residues: 1129 sheet: -0.75 (0.57), residues: 78 loop : -0.64 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.028 0.001 TYR T 30 ARG 0.009 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 960) hydrogen bonds : angle 4.26738 ( 2847) covalent geometry : bond 0.00318 (12323) covalent geometry : angle 0.60350 (16687) *********************** 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 332 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 293 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7816 (mm) REVERT: 4 63 PHE cc_start: 0.7940 (m-10) cc_final: 0.7720 (m-80) REVERT: 5 7 LYS cc_start: 0.7710 (mmtp) cc_final: 0.7449 (mmtp) REVERT: G 46 LEU cc_start: 0.8665 (mt) cc_final: 0.8360 (mm) REVERT: G 52 TYR cc_start: 0.7019 (m-80) cc_final: 0.6805 (m-80) REVERT: G 133 ARG cc_start: 0.8674 (ttt-90) cc_final: 0.7734 (tpp80) REVERT: G 147 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7985 (tp30) REVERT: G 189 SER cc_start: 0.7415 (t) cc_final: 0.7196 (p) REVERT: H 109 LYS cc_start: 0.8399 (mttm) cc_final: 0.8180 (mttm) REVERT: H 122 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7942 (p) REVERT: H 128 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8124 (mtp85) REVERT: K 87 GLU cc_start: 0.7771 (mp0) cc_final: 0.7569 (mp0) REVERT: N 36 TYR cc_start: 0.8202 (m-10) cc_final: 0.7690 (m-10) REVERT: N 147 ILE cc_start: 0.8900 (tp) cc_final: 0.8625 (tp) REVERT: N 159 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8841 (ttm170) REVERT: P 14 LYS cc_start: 0.8297 (tttm) cc_final: 0.8034 (tttm) REVERT: R 29 ILE cc_start: 0.8643 (mp) cc_final: 0.8142 (tp) REVERT: R 88 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8160 (mtp85) REVERT: S 31 TYR cc_start: 0.8433 (t80) cc_final: 0.8227 (t80) REVERT: S 53 LYS cc_start: 0.8219 (pttt) cc_final: 0.7967 (mmtt) outliers start: 39 outliers final: 29 residues processed: 314 average time/residue: 0.2521 time to fit residues: 110.1342 Evaluate side-chains 319 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR 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 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 G residue 182 ASN 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 171 MET Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 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 50 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124826 restraints weight = 17650.275| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.62 r_work: 0.3416 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12323 Z= 0.144 Angle : 0.608 9.475 16687 Z= 0.310 Chirality : 0.042 0.233 1971 Planarity : 0.004 0.047 2065 Dihedral : 4.379 55.622 1685 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.71 % Allowed : 23.46 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.21), residues: 1558 helix: 1.97 (0.15), residues: 1130 sheet: -0.71 (0.56), residues: 78 loop : -0.58 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.016 0.001 TYR N 212 ARG 0.005 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 960) hydrogen bonds : angle 4.22551 ( 2847) covalent geometry : bond 0.00309 (12323) covalent geometry : angle 0.60786 (16687) ********************** 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 324 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7847 (mm) REVERT: 5 7 LYS cc_start: 0.7658 (mmtp) cc_final: 0.7421 (mmtp) REVERT: G 46 LEU cc_start: 0.8596 (mt) cc_final: 0.8302 (mm) REVERT: G 133 ARG cc_start: 0.8625 (ttt-90) cc_final: 0.7703 (tpp80) REVERT: G 147 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7948 (tp30) REVERT: G 189 SER cc_start: 0.7454 (t) cc_final: 0.7250 (p) REVERT: H 109 LYS cc_start: 0.8418 (mttm) cc_final: 0.8206 (mttm) REVERT: H 122 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7871 (p) REVERT: H 128 ARG cc_start: 0.8597 (mtp85) cc_final: 0.8139 (mtp85) REVERT: K 26 TYR cc_start: 0.8570 (t80) cc_final: 0.8265 (t80) REVERT: M 145 ASP cc_start: 0.8668 (t0) cc_final: 0.8433 (t0) REVERT: N 36 TYR cc_start: 0.8192 (m-10) cc_final: 0.7680 (m-10) REVERT: N 147 ILE cc_start: 0.8908 (tp) cc_final: 0.8637 (tp) REVERT: N 159 ARG cc_start: 0.9080 (ttm110) cc_final: 0.8841 (ttm110) REVERT: P 14 LYS cc_start: 0.8333 (tttm) cc_final: 0.7991 (mtpt) REVERT: R 82 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8058 (mptt) REVERT: R 88 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8148 (mtp85) REVERT: S 53 LYS cc_start: 0.8220 (pttt) cc_final: 0.7954 (mmtt) outliers start: 34 outliers final: 32 residues processed: 307 average time/residue: 0.2630 time to fit residues: 111.8800 Evaluate side-chains 318 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 284 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 4 THR 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 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 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 140 MET Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 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 130 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** 5 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.159035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124113 restraints weight = 17601.349| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.50 r_work: 0.3406 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3891 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= 0.152 Angle : 0.609 9.293 16687 Z= 0.312 Chirality : 0.043 0.237 1971 Planarity : 0.004 0.046 2065 Dihedral : 4.377 54.679 1685 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.87 % Allowed : 23.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1558 helix: 1.96 (0.15), residues: 1129 sheet: -0.71 (0.56), residues: 78 loop : -0.62 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.031 0.001 TYR T 30 ARG 0.008 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 960) hydrogen bonds : angle 4.23807 ( 2847) covalent geometry : bond 0.00334 (12323) covalent geometry : angle 0.60948 (16687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7026.05 seconds wall clock time: 123 minutes 17.28 seconds (7397.28 seconds total)