Starting phenix.real_space_refine on Wed Jul 30 01:18:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9j_34569/07_2025/8h9j_34569.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9j_34569/07_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_34569/07_2025/8h9j_34569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9j_34569/07_2025/8h9j_34569.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9j_34569/07_2025/8h9j_34569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9j_34569/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.02, 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: 2.86 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: 1.38 Creating SS restraints... Processing helix chain '6' and resid 1 through 17 removed outlier: 4.121A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 39 Processing helix chain '7' and resid 42 through 73 Processing helix chain '8' and resid 2 through 17 removed outlier: 4.121A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 Processing helix chain '1' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 Processing helix chain '1' and resid 42 through 73 Processing helix chain '2' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 Processing helix chain '3' and resid 2 through 17 removed outlier: 4.121A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 Processing helix chain '4' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 Processing helix chain '5' and resid 2 through 17 removed outlier: 4.122A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 Processing helix chain 'G' and resid 33 through 48 removed outlier: 4.097A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 99 Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.339A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.538A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.966A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.956A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.635A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.631A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.540A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'N' and resid 5 through 10 removed outlier: 4.350A pdb=" N SER N 8 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.677A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 68 through 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.853A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.015A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 136 No H-bonds generated for 'chain 'N' and resid 134 through 136' Processing helix chain 'N' and resid 137 through 181 Proline residue: N 153 - end of helix removed outlier: 3.815A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 225 Processing helix chain 'P' and resid 4 through 9 removed outlier: 3.578A pdb=" N ASN P 8 " --> pdb=" O SER P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 20 removed outlier: 3.686A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.531A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.372A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 95 removed outlier: 3.502A pdb=" N ARG S 95 " --> pdb=" O ILE S 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 43 Proline residue: T 35 - end of helix Processing helix chain 'T' and resid 44 through 45 No H-bonds generated for 'chain 'T' and resid 44 through 45' Processing helix chain 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 9 through 22 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 removed outlier: 3.579A pdb=" N ASN Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.218A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 3.615A pdb=" N ALA H 31 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.113A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 966 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.13 Time building geometry restraints manager: 3.45 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: 13.950 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 32.110 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.000 ------------------------------------------------------------------------------- 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 : 1.229 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: 0.2575 time to fit residues: 140.7332 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 : 1.403 ------------------------------------------------------------------------------- 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 = 0.122923 restraints weight = 17712.362| |-----------------------------------------------------------------------------| 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 : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 75 MET cc_start: 0.7169 (tpp) cc_final: 0.6207 (mtt) REVERT: G 44 TYR cc_start: 0.8384 (t80) cc_final: 0.8123 (t80) REVERT: H 85 ASN cc_start: 0.7652 (m-40) cc_final: 0.7419 (m110) REVERT: H 102 MET cc_start: 0.5062 (ttm) cc_final: 0.4835 (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: 0.8716 (tmm) outliers start: 32 outliers final: 17 residues processed: 350 average time/residue: 0.2394 time to fit residues: 117.9165 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 : 1.156 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.158991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123982 restraints weight = 17851.564| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.49 r_work: 0.3408 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 12323 Z= 0.156 Angle : 0.584 8.510 16687 Z= 0.306 Chirality : 0.042 0.172 1971 Planarity : 0.004 0.050 2065 Dihedral : 4.495 58.656 1685 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.87 % Allowed : 18.44 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.21), residues: 1558 helix: 1.05 (0.15), residues: 1149 sheet: -1.33 (0.57), residues: 72 loop : -1.30 (0.33), residues: 337 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 0.033 0.002 PHE 2 69 TYR 0.017 0.001 TYR T 30 ARG 0.007 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.05467 ( 960) hydrogen bonds : angle 4.50041 ( 2847) covalent geometry : bond 0.00330 (12323) covalent geometry : angle 0.58359 (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 353 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 7 LYS cc_start: 0.7715 (mmtp) cc_final: 0.7321 (mmtp) REVERT: G 37 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6779 (mt-10) REVERT: G 44 TYR cc_start: 0.8392 (t80) cc_final: 0.8155 (t80) REVERT: G 211 ASN cc_start: 0.8936 (m-40) cc_final: 0.8644 (t0) REVERT: N 36 TYR cc_start: 0.8188 (m-10) cc_final: 0.7621 (m-10) REVERT: R 29 ILE cc_start: 0.8794 (mp) cc_final: 0.8306 (tp) REVERT: R 88 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8153 (mtp85) outliers start: 36 outliers final: 23 residues processed: 332 average time/residue: 0.2495 time to fit residues: 116.2776 Evaluate side-chains 317 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 294 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 33 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.159416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123935 restraints weight = 17656.260| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.67 r_work: 0.3408 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 12323 Z= 0.151 Angle : 0.566 7.524 16687 Z= 0.298 Chirality : 0.042 0.175 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.463 57.806 1685 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.59 % Allowed : 18.60 % 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: 1.45 (0.15), residues: 1148 sheet: -1.13 (0.57), residues: 72 loop : -1.10 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.027 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 4.38425 ( 2847) covalent geometry : bond 0.00327 (12323) covalent geometry : angle 0.56584 (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 354 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7791 (mm) REVERT: 4 63 PHE cc_start: 0.7863 (m-10) cc_final: 0.7535 (m-10) REVERT: 5 7 LYS cc_start: 0.7668 (mmtp) cc_final: 0.7324 (mmtp) REVERT: G 37 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6732 (mt-10) REVERT: G 44 TYR cc_start: 0.8237 (t80) cc_final: 0.7899 (t80) REVERT: G 147 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8032 (tp30) REVERT: G 211 ASN cc_start: 0.8902 (m-40) cc_final: 0.8588 (t0) REVERT: H 128 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8325 (mtp85) REVERT: K 51 TYR cc_start: 0.8957 (t80) cc_final: 0.8751 (t80) REVERT: K 87 GLU cc_start: 0.7740 (mp0) cc_final: 0.7421 (mp0) REVERT: N 36 TYR cc_start: 0.8182 (m-10) cc_final: 0.7676 (m-10) REVERT: P 14 LYS cc_start: 0.8237 (tttm) cc_final: 0.7882 (mtpt) REVERT: R 28 TRP cc_start: 0.8450 (t60) cc_final: 0.8175 (t60) REVERT: R 29 ILE cc_start: 0.8803 (mp) cc_final: 0.8253 (tp) REVERT: R 88 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8150 (mtp85) REVERT: T 30 TYR cc_start: 0.6474 (t80) cc_final: 0.6262 (t80) outliers start: 45 outliers final: 30 residues processed: 328 average time/residue: 0.2532 time to fit residues: 116.7492 Evaluate side-chains 325 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 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 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: 0.0870 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.160185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.125059 restraints weight = 17741.528| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.53 r_work: 0.3420 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3219 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= 0.141 Angle : 0.565 7.679 16687 Z= 0.294 Chirality : 0.041 0.192 1971 Planarity : 0.004 0.044 2065 Dihedral : 4.405 55.420 1685 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.07 % Allowed : 19.39 % 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 : -1.01 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.001 PHE R 79 TYR 0.021 0.001 TYR T 30 ARG 0.010 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 960) hydrogen bonds : angle 4.29547 ( 2847) covalent geometry : bond 0.00290 (12323) covalent geometry : angle 0.56533 (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 352 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 1.684 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: 0.8070 (OUTLIER) cc_final: 0.7813 (mm) REVERT: 4 63 PHE cc_start: 0.7860 (m-10) cc_final: 0.7489 (m-10) REVERT: 5 7 LYS cc_start: 0.7678 (mmtp) cc_final: 0.7345 (mmtp) REVERT: G 37 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6784 (mt-10) REVERT: G 44 TYR cc_start: 0.8146 (t80) cc_final: 0.7797 (t80) REVERT: G 147 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8020 (tp30) REVERT: G 211 ASN cc_start: 0.8891 (m-40) cc_final: 0.8626 (t0) REVERT: H 128 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8249 (mtp85) REVERT: K 51 TYR cc_start: 0.8971 (t80) cc_final: 0.8755 (t80) REVERT: K 87 GLU cc_start: 0.7728 (mp0) cc_final: 0.7493 (mp0) REVERT: N 36 TYR cc_start: 0.8166 (m-10) cc_final: 0.7692 (m-10) REVERT: P 14 LYS cc_start: 0.8277 (tttm) cc_final: 0.7931 (mtpt) REVERT: R 29 ILE cc_start: 0.8773 (mp) cc_final: 0.8302 (tp) outliers start: 51 outliers final: 32 residues processed: 322 average time/residue: 0.3572 time to fit residues: 161.0166 Evaluate side-chains 327 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 2.507 ------------------------------------------------------------------------------- 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 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 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 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 R residue 89 LEU Chi-restraints excluded: chain S residue 44 GLU 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: 0.6980 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN N 4 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 ASN S 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.159811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124690 restraints weight = 17884.531| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.54 r_work: 0.3411 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 12323 Z= 0.150 Angle : 0.578 7.596 16687 Z= 0.300 Chirality : 0.042 0.197 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.375 54.458 1685 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.67 % Allowed : 21.31 % Favored : 75.02 % 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: 1.66 (0.21), residues: 1558 helix: 1.81 (0.15), residues: 1143 sheet: -0.74 (0.56), residues: 80 loop : -0.84 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.001 PHE R 79 TYR 0.029 0.001 TYR T 30 ARG 0.008 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 960) hydrogen bonds : angle 4.27737 ( 2847) covalent geometry : bond 0.00328 (12323) covalent geometry : angle 0.57832 (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 343 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7806 (mm) REVERT: 4 63 PHE cc_start: 0.7871 (m-10) cc_final: 0.7553 (m-10) REVERT: 5 7 LYS cc_start: 0.7646 (mmtp) cc_final: 0.7352 (mmtp) REVERT: G 37 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6786 (mt-10) REVERT: G 44 TYR cc_start: 0.8161 (t80) cc_final: 0.7792 (t80) REVERT: G 46 LEU cc_start: 0.8712 (mt) cc_final: 0.8382 (mm) REVERT: G 147 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8006 (tp30) REVERT: G 211 ASN cc_start: 0.8883 (m-40) cc_final: 0.8599 (t0) REVERT: H 128 ARG cc_start: 0.8572 (mtp85) cc_final: 0.8287 (mtp85) REVERT: K 51 TYR cc_start: 0.8986 (t80) cc_final: 0.8743 (t80) REVERT: K 87 GLU cc_start: 0.7733 (mp0) cc_final: 0.7492 (mp0) REVERT: N 36 TYR cc_start: 0.8161 (m-10) cc_final: 0.7745 (m-10) REVERT: N 159 ARG cc_start: 0.9121 (ttm110) cc_final: 0.8905 (ttm170) REVERT: P 14 LYS cc_start: 0.8219 (tttm) cc_final: 0.7866 (mtpt) REVERT: R 28 TRP cc_start: 0.8486 (t60) cc_final: 0.8237 (t60) REVERT: R 29 ILE cc_start: 0.8740 (mp) cc_final: 0.8228 (tp) REVERT: S 31 TYR cc_start: 0.8392 (t80) cc_final: 0.8089 (t80) REVERT: S 44 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: T 13 LEU cc_start: 0.6755 (mm) cc_final: 0.6551 (mm) outliers start: 46 outliers final: 34 residues processed: 320 average time/residue: 0.2681 time to fit residues: 121.2547 Evaluate side-chains 322 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 286 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 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 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 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 5 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 44 GLU 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: 6.9990 chunk 80 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN 8 45 GLN 3 45 GLN ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121115 restraints weight = 17916.004| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.50 r_work: 0.3366 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12323 Z= 0.197 Angle : 0.625 10.327 16687 Z= 0.322 Chirality : 0.044 0.209 1971 Planarity : 0.004 0.043 2065 Dihedral : 4.453 58.632 1685 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.39 % Allowed : 21.15 % Favored : 74.46 % 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: 1.63 (0.21), residues: 1558 helix: 1.77 (0.15), residues: 1143 sheet: -0.78 (0.56), residues: 80 loop : -0.77 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.002 PHE R 79 TYR 0.040 0.002 TYR T 30 ARG 0.003 0.000 ARG N 159 Details of bonding type rmsd hydrogen bonds : bond 0.05375 ( 960) hydrogen bonds : angle 4.35678 ( 2847) covalent geometry : bond 0.00454 (12323) covalent geometry : angle 0.62473 (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 345 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7806 (mm) REVERT: 1 60 MET cc_start: 0.7206 (mmt) cc_final: 0.6699 (mmt) REVERT: 4 63 PHE cc_start: 0.7975 (m-10) cc_final: 0.7707 (m-80) REVERT: 5 7 LYS cc_start: 0.7703 (mmtp) cc_final: 0.7417 (mmtp) REVERT: G 37 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6787 (mt-10) REVERT: G 44 TYR cc_start: 0.8295 (t80) cc_final: 0.8040 (t80) REVERT: G 46 LEU cc_start: 0.8722 (mt) cc_final: 0.8390 (mm) REVERT: G 147 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8017 (tp30) REVERT: G 211 ASN cc_start: 0.8909 (m-40) cc_final: 0.8700 (m-40) REVERT: H 122 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7845 (p) REVERT: H 128 ARG cc_start: 0.8606 (mtp85) cc_final: 0.8110 (mtp85) REVERT: K 87 GLU cc_start: 0.7802 (mp0) cc_final: 0.7562 (mp0) REVERT: N 36 TYR cc_start: 0.8195 (m-10) cc_final: 0.7832 (m-10) REVERT: P 14 LYS cc_start: 0.8260 (tttm) cc_final: 0.7992 (tttm) REVERT: R 69 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7150 (mp) REVERT: S 31 TYR cc_start: 0.8426 (t80) cc_final: 0.8148 (t80) REVERT: S 44 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7766 (mm-30) outliers start: 55 outliers final: 39 residues processed: 322 average time/residue: 0.2449 time to fit residues: 110.8376 Evaluate side-chains 329 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 32 LEU Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 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 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 P residue 11 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 44 GLU 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: 1.9990 chunk 72 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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** K 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.156384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121515 restraints weight = 18010.830| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.52 r_work: 0.3372 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12323 Z= 0.185 Angle : 0.626 9.734 16687 Z= 0.322 Chirality : 0.043 0.218 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.489 59.989 1685 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.99 % Allowed : 22.51 % Favored : 73.50 % 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: 1.78 (0.15), residues: 1143 sheet: -0.77 (0.57), residues: 80 loop : -0.73 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 28 HIS 0.007 0.001 HIS N 127 PHE 0.026 0.002 PHE R 79 TYR 0.040 0.001 TYR T 30 ARG 0.009 0.000 ARG T 36 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 960) hydrogen bonds : angle 4.34215 ( 2847) covalent geometry : bond 0.00423 (12323) covalent geometry : angle 0.62568 (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 341 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 291 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7833 (mm) REVERT: 8 58 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6882 (tm-30) REVERT: 1 60 MET cc_start: 0.7269 (mmt) cc_final: 0.6786 (mmt) REVERT: 2 58 GLU cc_start: 0.7922 (tp30) cc_final: 0.7600 (tp30) REVERT: 3 60 MET cc_start: 0.7417 (mmm) cc_final: 0.7117 (mmm) REVERT: 4 63 PHE cc_start: 0.7982 (m-10) cc_final: 0.7702 (m-80) REVERT: 5 7 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7443 (mmtp) REVERT: G 44 TYR cc_start: 0.8269 (t80) cc_final: 0.8051 (t80) REVERT: G 46 LEU cc_start: 0.8723 (mt) cc_final: 0.8395 (mm) REVERT: G 147 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8010 (tp30) REVERT: G 189 SER cc_start: 0.7439 (t) cc_final: 0.7181 (p) REVERT: H 109 LYS cc_start: 0.8356 (mttm) cc_final: 0.8152 (mttm) REVERT: H 122 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7869 (p) REVERT: H 128 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8150 (mtp85) REVERT: K 87 GLU cc_start: 0.7768 (mp0) cc_final: 0.7540 (mp0) REVERT: N 36 TYR cc_start: 0.8199 (m-10) cc_final: 0.7846 (m-10) REVERT: N 159 ARG cc_start: 0.9111 (ttm110) cc_final: 0.8870 (ttm170) REVERT: P 14 LYS cc_start: 0.8307 (tttm) cc_final: 0.8049 (tttm) REVERT: R 28 TRP cc_start: 0.8501 (t60) cc_final: 0.8217 (t60) REVERT: R 69 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7084 (mp) REVERT: S 31 TYR cc_start: 0.8429 (t80) cc_final: 0.8206 (t80) REVERT: T 33 LEU cc_start: 0.2410 (OUTLIER) cc_final: 0.2184 (tt) outliers start: 50 outliers final: 36 residues processed: 321 average time/residue: 0.2574 time to fit residues: 115.6215 Evaluate side-chains 323 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 283 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 8 residue 27 THR Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 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 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 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 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 P residue 11 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 T residue 33 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: 0.7980 chunk 13 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125541 restraints weight = 17766.921| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.43 r_work: 0.3430 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12323 Z= 0.141 Angle : 0.592 9.455 16687 Z= 0.303 Chirality : 0.042 0.225 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.364 55.993 1685 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.43 % Allowed : 23.38 % Favored : 73.18 % 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: 1.92 (0.22), residues: 1558 helix: 1.99 (0.15), residues: 1135 sheet: -0.76 (0.57), residues: 78 loop : -0.62 (0.35), residues: 345 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 0.036 0.001 TYR T 30 ARG 0.004 0.000 ARG G 118 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 960) hydrogen bonds : angle 4.22532 ( 2847) covalent geometry : bond 0.00299 (12323) covalent geometry : angle 0.59152 (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 330 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7850 (mm) REVERT: 4 63 PHE cc_start: 0.7901 (m-10) cc_final: 0.7662 (m-80) REVERT: 5 7 LYS cc_start: 0.7671 (mmtp) cc_final: 0.7436 (mmtp) REVERT: G 46 LEU cc_start: 0.8610 (mt) cc_final: 0.8309 (mm) REVERT: G 133 ARG cc_start: 0.8654 (ttt-90) cc_final: 0.7718 (tpp80) REVERT: G 147 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8001 (tp30) REVERT: G 189 SER cc_start: 0.7448 (t) cc_final: 0.7220 (p) REVERT: H 109 LYS cc_start: 0.8435 (mttm) cc_final: 0.8201 (mttm) REVERT: H 122 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7963 (p) REVERT: H 128 ARG cc_start: 0.8569 (mtp85) cc_final: 0.8105 (mtp85) REVERT: K 26 TYR cc_start: 0.8533 (t80) cc_final: 0.8238 (t80) REVERT: M 145 ASP cc_start: 0.8688 (t0) cc_final: 0.8466 (t0) REVERT: N 36 TYR cc_start: 0.8167 (m-10) cc_final: 0.7846 (m-10) REVERT: N 147 ILE cc_start: 0.8896 (tp) cc_final: 0.8626 (tp) REVERT: P 14 LYS cc_start: 0.8291 (tttm) cc_final: 0.7946 (mtpt) REVERT: R 28 TRP cc_start: 0.8525 (t60) cc_final: 0.8237 (t60) REVERT: R 29 ILE cc_start: 0.8636 (mp) cc_final: 0.8068 (tp) REVERT: R 82 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8062 (mptt) REVERT: T 13 LEU cc_start: 0.6776 (mm) cc_final: 0.6560 (mm) outliers start: 43 outliers final: 33 residues processed: 310 average time/residue: 0.2781 time to fit residues: 119.5312 Evaluate side-chains 315 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 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 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 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 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 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: 0.8980 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.124899 restraints weight = 17620.136| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.47 r_work: 0.3414 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12323 Z= 0.147 Angle : 0.611 10.220 16687 Z= 0.312 Chirality : 0.042 0.243 1971 Planarity : 0.004 0.042 2065 Dihedral : 4.355 53.530 1685 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.79 % Allowed : 24.02 % Favored : 73.18 % 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: 1.93 (0.22), residues: 1558 helix: 2.00 (0.15), residues: 1135 sheet: -1.11 (0.54), residues: 85 loop : -0.52 (0.35), residues: 338 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 0.025 0.001 PHE R 79 TYR 0.033 0.001 TYR T 30 ARG 0.008 0.000 ARG I 24 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 960) hydrogen bonds : angle 4.25526 ( 2847) covalent geometry : bond 0.00319 (12323) covalent geometry : angle 0.61109 (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 317 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 71 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7866 (mm) REVERT: 5 7 LYS cc_start: 0.7643 (mmtp) cc_final: 0.7410 (mmtp) REVERT: G 46 LEU cc_start: 0.8595 (mt) cc_final: 0.8308 (mm) REVERT: G 133 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.7723 (tpp80) REVERT: G 147 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7962 (tp30) REVERT: G 189 SER cc_start: 0.7423 (t) cc_final: 0.7219 (p) REVERT: H 109 LYS cc_start: 0.8419 (mttm) cc_final: 0.8215 (mttm) REVERT: H 122 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7942 (p) REVERT: H 128 ARG cc_start: 0.8594 (mtp85) cc_final: 0.8183 (mtp85) REVERT: K 26 TYR cc_start: 0.8548 (t80) cc_final: 0.8267 (t80) REVERT: K 87 GLU cc_start: 0.7791 (mp0) cc_final: 0.7418 (mp0) REVERT: M 145 ASP cc_start: 0.8663 (t0) cc_final: 0.8422 (t0) REVERT: N 36 TYR cc_start: 0.8154 (m-10) cc_final: 0.7841 (m-10) REVERT: N 147 ILE cc_start: 0.8912 (tp) cc_final: 0.8634 (tp) REVERT: P 14 LYS cc_start: 0.8291 (tttm) cc_final: 0.7939 (mtpt) REVERT: R 28 TRP cc_start: 0.8537 (t60) cc_final: 0.8024 (t60) REVERT: R 29 ILE cc_start: 0.8615 (mp) cc_final: 0.8072 (tp) REVERT: R 82 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8067 (mptt) REVERT: T 13 LEU cc_start: 0.6701 (mm) cc_final: 0.6489 (mm) outliers start: 35 outliers final: 31 residues processed: 299 average time/residue: 0.2765 time to fit residues: 114.2318 Evaluate side-chains 311 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 8 residue 28 VAL Chi-restraints excluded: chain 8 residue 54 PHE Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 18 VAL Chi-restraints excluded: chain 2 residue 31 SER Chi-restraints excluded: chain 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 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 71 ILE Chi-restraints excluded: chain 5 residue 72 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 114 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain N residue 14 ILE Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain Q residue 11 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 130 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 69 optimal weight: 0.0270 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN G 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.159309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.124275 restraints weight = 17561.999| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.44 r_work: 0.3409 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 0.063 12323 Z= 0.154 Angle : 0.609 9.359 16687 Z= 0.313 Chirality : 0.043 0.242 1971 Planarity : 0.004 0.050 2065 Dihedral : 4.336 51.767 1685 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.79 % Allowed : 24.26 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.22), residues: 1558 helix: 2.00 (0.15), residues: 1135 sheet: -1.08 (0.54), residues: 85 loop : -0.54 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 28 HIS 0.006 0.001 HIS N 127 PHE 0.025 0.001 PHE R 79 TYR 0.032 0.001 TYR T 30 ARG 0.008 0.001 ARG I 24 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 960) hydrogen bonds : angle 4.24244 ( 2847) covalent geometry : bond 0.00339 (12323) covalent geometry : angle 0.60921 (16687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6967.90 seconds wall clock time: 124 minutes 54.41 seconds (7494.41 seconds total)