Starting phenix.real_space_refine on Sat Aug 23 11:57:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9q_34577/08_2025/8h9q_34577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9q_34577/08_2025/8h9q_34577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h9q_34577/08_2025/8h9q_34577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9q_34577/08_2025/8h9q_34577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9q_34577/08_2025/8h9q_34577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9q_34577/08_2025/8h9q_34577.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12083 Number of models: 1 Model: "" Number of chains: 19 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: "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: "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: "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} 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: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} 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 Time building chain proxies: 2.66, per 1000 atoms: 0.22 Number of scatterers: 12083 At special positions: 0 Unit cell: (107.31, 112.42, 140.16, 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 2158 8.00 N 1932 7.00 C 7930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 493.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 4 sheets defined 76.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain '4' and resid 1 through 17 removed outlier: 3.956A 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 removed outlier: 3.874A pdb=" N ALA 4 59 " --> pdb=" O ALA 4 55 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 17 removed outlier: 3.956A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 removed outlier: 3.829A pdb=" N ILE 5 33 " --> pdb=" O PHE 5 29 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 73 removed outlier: 3.875A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 3.955A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 removed outlier: 3.507A pdb=" N ILE 6 33 " --> pdb=" O PHE 6 29 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 removed outlier: 3.874A pdb=" N ALA 6 59 " --> pdb=" O ALA 6 55 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 17 removed outlier: 3.955A 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 removed outlier: 3.874A pdb=" N ALA 7 59 " --> pdb=" O ALA 7 55 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.956A 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 removed outlier: 3.874A pdb=" N ALA 8 59 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 17 removed outlier: 3.956A 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 removed outlier: 3.524A pdb=" N TYR 1 49 " --> pdb=" O GLN 1 45 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 3.956A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 removed outlier: 3.566A pdb=" N ILE 2 33 " --> pdb=" O PHE 2 29 " (cutoff:3.500A) Processing helix chain '2' and resid 42 through 73 removed outlier: 3.874A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 17 removed outlier: 3.955A 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 removed outlier: 3.874A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 56 removed outlier: 4.275A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 4.485A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.706A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.662A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 191 Processing helix chain 'G' and resid 197 through 221 removed outlier: 3.509A pdb=" N THR G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) 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: 3.725A 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 9 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.415A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.542A 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: 4.696A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.769A 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 '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: 3.700A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 87 removed outlier: 3.506A pdb=" N ALA N 80 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 removed outlier: 3.504A pdb=" N ASN N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Proline residue: N 107 - end of helix removed outlier: 3.899A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 127 Processing helix chain 'N' and resid 134 through 138 removed outlier: 3.731A pdb=" N LEU N 137 " --> pdb=" O PRO N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 181 removed outlier: 4.119A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.645A 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 9 through 19 removed outlier: 4.077A pdb=" N MET P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Proline residue: P 15 - end of helix removed outlier: 3.699A 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 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 8 through 21 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.942A 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 85 removed outlier: 4.468A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS R 82 " --> pdb=" O SER R 78 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N HIS R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.332A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) 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 94 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 4.030A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.251A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS I 44 " --> pdb=" O LYS G 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 6.180A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.295A 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 13 948 hydrogen bonds defined for protein. 2796 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: 1.62 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3719 1.34 - 1.46: 2331 1.46 - 1.57: 6159 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12324 Sorted by residual: bond pdb=" N LEU 7 42 " pdb=" CA LEU 7 42 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.30e+00 bond pdb=" N LEU 2 42 " pdb=" CA LEU 2 42 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.93e+00 bond pdb=" N LEU 3 42 " pdb=" CA LEU 3 42 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.18e-02 7.18e+03 7.65e+00 bond pdb=" N VAL 2 28 " pdb=" CA VAL 2 28 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.37e+00 bond pdb=" N VAL 1 28 " pdb=" CA VAL 1 28 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 7.11e+00 ... (remaining 12319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 15546 1.33 - 2.67: 920 2.67 - 4.00: 186 4.00 - 5.34: 29 5.34 - 6.67: 8 Bond angle restraints: 16689 Sorted by residual: angle pdb=" C ILE N 138 " pdb=" CA ILE N 138 " pdb=" CB ILE N 138 " ideal model delta sigma weight residual 113.70 110.15 3.55 9.50e-01 1.11e+00 1.39e+01 angle pdb=" N ILE P 6 " pdb=" CA ILE P 6 " pdb=" C ILE P 6 " ideal model delta sigma weight residual 112.98 108.68 4.30 1.25e+00 6.40e-01 1.18e+01 angle pdb=" N LEU 8 42 " pdb=" CA LEU 8 42 " pdb=" C LEU 8 42 " ideal model delta sigma weight residual 112.72 108.93 3.79 1.14e+00 7.69e-01 1.10e+01 angle pdb=" N LYS R 91 " pdb=" CA LYS R 91 " pdb=" C LYS R 91 " ideal model delta sigma weight residual 114.56 110.38 4.18 1.27e+00 6.20e-01 1.08e+01 angle pdb=" C ILE S 45 " pdb=" CA ILE S 45 " pdb=" CB ILE S 45 " ideal model delta sigma weight residual 114.35 110.88 3.47 1.06e+00 8.90e-01 1.07e+01 ... (remaining 16684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6562 17.97 - 35.95: 580 35.95 - 53.92: 78 53.92 - 71.90: 24 71.90 - 89.87: 5 Dihedral angle restraints: 7249 sinusoidal: 2711 harmonic: 4538 Sorted by residual: dihedral pdb=" CA TYR G 193 " pdb=" C TYR G 193 " pdb=" N ASP G 194 " pdb=" CA ASP G 194 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CB GLU G 92 " pdb=" CG GLU G 92 " pdb=" CD GLU G 92 " pdb=" OE1 GLU G 92 " ideal model delta sinusoidal sigma weight residual 0.00 87.48 -87.48 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA ASP G 140 " pdb=" CB ASP G 140 " pdb=" CG ASP G 140 " pdb=" OD1 ASP G 140 " ideal model delta sinusoidal sigma weight residual -30.00 -83.84 53.84 1 2.00e+01 2.50e-03 9.84e+00 ... (remaining 7246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1381 0.042 - 0.083: 418 0.083 - 0.125: 126 0.125 - 0.167: 31 0.167 - 0.209: 15 Chirality restraints: 1971 Sorted by residual: chirality pdb=" CA ILE 2 25 " pdb=" N ILE 2 25 " pdb=" C ILE 2 25 " pdb=" CB ILE 2 25 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE 8 25 " pdb=" N ILE 8 25 " pdb=" C ILE 8 25 " pdb=" CB ILE 8 25 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE 3 25 " pdb=" N ILE 3 25 " pdb=" C ILE 3 25 " pdb=" CB ILE 3 25 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1968 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 38 " 0.197 9.50e-02 1.11e+02 8.82e-02 4.77e+00 pdb=" NE ARG 5 38 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG 5 38 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 38 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 7 40 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C PRO 7 40 " 0.036 2.00e-02 2.50e+03 pdb=" O PRO 7 40 " -0.014 2.00e-02 2.50e+03 pdb=" N SER 7 41 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO 5 40 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C PRO 5 40 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO 5 40 " 0.013 2.00e-02 2.50e+03 pdb=" N SER 5 41 " 0.011 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1315 2.74 - 3.28: 13903 3.28 - 3.82: 20522 3.82 - 4.36: 24448 4.36 - 4.90: 41091 Nonbonded interactions: 101279 Sorted by model distance: nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR G 214 " pdb=" O PRO H 23 " model vdw 2.221 3.040 nonbonded pdb=" O ARG H 134 " pdb=" ND2 ASN H 138 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR G 44 " pdb=" OD1 ASN G 211 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR R 50 " pdb=" O GLY R 64 " model vdw 2.254 3.040 ... (remaining 101274 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: 9.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 : 0.005 0.039 12324 Z= 0.318 Angle : 0.732 6.674 16689 Z= 0.480 Chirality : 0.048 0.209 1971 Planarity : 0.005 0.088 2066 Dihedral : 13.533 89.871 4353 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.19), residues: 1558 helix: -1.76 (0.13), residues: 1126 sheet: -1.94 (0.47), residues: 87 loop : -2.04 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 38 TYR 0.016 0.001 TYR G 193 PHE 0.018 0.001 PHE H 45 TRP 0.005 0.001 TRP N 48 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00520 (12324) covalent geometry : angle 0.73180 (16689) hydrogen bonds : bond 0.16933 ( 942) hydrogen bonds : angle 7.24291 ( 2796) *********************** 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 548 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 39 ASN cc_start: 0.7857 (t0) cc_final: 0.7597 (t0) REVERT: 8 45 GLN cc_start: 0.7416 (tp40) cc_final: 0.7169 (tp40) REVERT: 1 2 ILE cc_start: 0.6704 (tt) cc_final: 0.6475 (tp) REVERT: 3 62 LEU cc_start: 0.8459 (mt) cc_final: 0.8175 (mt) REVERT: G 104 MET cc_start: 0.7510 (mmt) cc_final: 0.7006 (mmm) REVERT: G 156 ASP cc_start: 0.8075 (t0) cc_final: 0.7590 (t70) REVERT: G 222 THR cc_start: 0.7707 (m) cc_final: 0.7463 (m) REVERT: H 111 ASN cc_start: 0.8632 (m110) cc_final: 0.8196 (m-40) REVERT: H 135 ILE cc_start: 0.8815 (mt) cc_final: 0.8201 (mm) REVERT: H 139 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7771 (mp0) REVERT: I 14 ARG cc_start: 0.7950 (tpt90) cc_final: 0.7523 (ttm-80) REVERT: K 26 TYR cc_start: 0.7554 (t80) cc_final: 0.6723 (t80) REVERT: K 72 LYS cc_start: 0.8633 (mttt) cc_final: 0.8027 (mmtt) REVERT: K 89 LYS cc_start: 0.8485 (tttt) cc_final: 0.8256 (ttpt) REVERT: M 159 ASN cc_start: 0.7904 (p0) cc_final: 0.7619 (p0) REVERT: N 48 TRP cc_start: 0.8713 (t60) cc_final: 0.8351 (t60) REVERT: N 55 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8440 (mtmt) REVERT: N 145 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7796 (mm-30) REVERT: P 7 LYS cc_start: 0.8315 (tttm) cc_final: 0.8046 (tttm) REVERT: P 23 GLU cc_start: 0.8868 (mp0) cc_final: 0.8519 (mp0) REVERT: Q 3 GLN cc_start: 0.9017 (mp10) cc_final: 0.8670 (mp10) REVERT: Q 22 LEU cc_start: 0.9044 (tt) cc_final: 0.8794 (tp) REVERT: Q 26 LEU cc_start: 0.8975 (mt) cc_final: 0.8621 (mt) REVERT: R 28 TRP cc_start: 0.7161 (t-100) cc_final: 0.6730 (t60) REVERT: R 45 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7117 (ttt180) REVERT: R 49 ARG cc_start: 0.7106 (ttm170) cc_final: 0.6750 (ttt-90) REVERT: S 70 LYS cc_start: 0.6891 (tptt) cc_final: 0.6623 (tppt) REVERT: S 90 GLU cc_start: 0.8376 (tt0) cc_final: 0.7498 (tm-30) REVERT: T 16 TYR cc_start: 0.7299 (m-80) cc_final: 0.6898 (m-10) REVERT: T 21 LEU cc_start: 0.8615 (mt) cc_final: 0.8338 (pp) REVERT: T 29 ARG cc_start: 0.7947 (ttt180) cc_final: 0.7696 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.1138 time to fit residues: 86.9042 Evaluate side-chains 413 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.0060 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.2432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 120 HIS G 163 ASN G 202 GLN H 111 ASN N 46 GLN N 47 GLN N 172 HIS ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS S 75 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.146261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.117883 restraints weight = 22718.776| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.59 r_work: 0.3515 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12324 Z= 0.165 Angle : 0.680 8.615 16689 Z= 0.338 Chirality : 0.043 0.230 1971 Planarity : 0.004 0.045 2066 Dihedral : 4.121 19.798 1686 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.55 % Allowed : 16.44 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.21), residues: 1558 helix: 0.46 (0.15), residues: 1108 sheet: -1.23 (0.52), residues: 83 loop : -1.40 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 88 TYR 0.015 0.001 TYR R 47 PHE 0.017 0.002 PHE P 33 TRP 0.009 0.001 TRP N 68 HIS 0.004 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00323 (12324) covalent geometry : angle 0.67954 (16689) hydrogen bonds : bond 0.06049 ( 942) hydrogen bonds : angle 4.75878 ( 2796) *********************** 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 467 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 435 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 49 TYR cc_start: 0.7806 (m-10) cc_final: 0.7486 (m-80) REVERT: 6 60 MET cc_start: 0.6828 (mmm) cc_final: 0.6619 (mmm) REVERT: 7 39 ASN cc_start: 0.8198 (t0) cc_final: 0.7899 (t0) REVERT: 1 73 PHE cc_start: 0.7605 (m-10) cc_final: 0.7244 (m-80) REVERT: G 104 MET cc_start: 0.7773 (mmt) cc_final: 0.7315 (mmm) REVERT: G 222 THR cc_start: 0.7620 (m) cc_final: 0.7340 (m) REVERT: I 14 ARG cc_start: 0.7958 (tpt90) cc_final: 0.7605 (ttm-80) REVERT: I 18 ILE cc_start: 0.8995 (mt) cc_final: 0.8716 (mm) REVERT: K 26 TYR cc_start: 0.7608 (t80) cc_final: 0.6909 (t80) REVERT: K 72 LYS cc_start: 0.8718 (mttt) cc_final: 0.8122 (mmtt) REVERT: M 128 ASP cc_start: 0.8811 (p0) cc_final: 0.8438 (p0) REVERT: M 159 ASN cc_start: 0.7979 (p0) cc_final: 0.7629 (p0) REVERT: N 55 LYS cc_start: 0.9219 (mtpp) cc_final: 0.8790 (mtmt) REVERT: N 145 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7795 (mm-30) REVERT: N 152 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8667 (mm-40) REVERT: P 22 GLN cc_start: 0.8209 (pt0) cc_final: 0.7964 (pt0) REVERT: Q 29 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9146 (mm) REVERT: R 28 TRP cc_start: 0.7051 (t-100) cc_final: 0.6549 (t60) REVERT: R 45 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7073 (ttt180) REVERT: R 49 ARG cc_start: 0.7181 (ttm170) cc_final: 0.6879 (ttt-90) REVERT: S 70 LYS cc_start: 0.6819 (tptt) cc_final: 0.6571 (tppt) REVERT: S 90 GLU cc_start: 0.8424 (tt0) cc_final: 0.7452 (tm-30) REVERT: T 29 ARG cc_start: 0.8133 (ttt180) cc_final: 0.7812 (tpp-160) outliers start: 32 outliers final: 13 residues processed: 448 average time/residue: 0.1078 time to fit residues: 68.8231 Evaluate side-chains 399 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 385 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain T residue 36 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 17 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 101 optimal weight: 0.0040 chunk 74 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 45 GLN 2 39 ASN G 202 GLN H 32 ASN H 85 ASN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.142838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114459 restraints weight = 23416.302| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.61 r_work: 0.3462 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12324 Z= 0.182 Angle : 0.665 11.652 16689 Z= 0.331 Chirality : 0.043 0.215 1971 Planarity : 0.004 0.055 2066 Dihedral : 4.123 18.031 1686 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.87 % Allowed : 18.83 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.21), residues: 1558 helix: 1.18 (0.15), residues: 1102 sheet: -0.90 (0.54), residues: 85 loop : -0.96 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 39 TYR 0.016 0.002 TYR G 44 PHE 0.019 0.002 PHE 3 54 TRP 0.007 0.001 TRP P 25 HIS 0.006 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00405 (12324) covalent geometry : angle 0.66490 (16689) hydrogen bonds : bond 0.05474 ( 942) hydrogen bonds : angle 4.54761 ( 2796) *********************** 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 450 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 414 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8628 (t) cc_final: 0.8195 (m) REVERT: 6 49 TYR cc_start: 0.7962 (m-10) cc_final: 0.7670 (m-80) REVERT: 1 62 LEU cc_start: 0.7890 (mt) cc_final: 0.7446 (mt) REVERT: 2 75 MET cc_start: 0.6275 (mmm) cc_final: 0.5527 (mmt) REVERT: 3 1 ASP cc_start: 0.7147 (p0) cc_final: 0.6591 (t70) REVERT: G 36 ARG cc_start: 0.8143 (ttt180) cc_final: 0.7921 (tmm160) REVERT: G 104 MET cc_start: 0.7980 (mmt) cc_final: 0.7545 (mmm) REVERT: H 25 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7540 (tm-30) REVERT: H 32 ASN cc_start: 0.8321 (m-40) cc_final: 0.7620 (t0) REVERT: I 14 ARG cc_start: 0.8044 (tpt90) cc_final: 0.7454 (ttm-80) REVERT: K 26 TYR cc_start: 0.7642 (t80) cc_final: 0.6865 (t80) REVERT: K 87 GLU cc_start: 0.8597 (pp20) cc_final: 0.8283 (pt0) REVERT: M 159 ASN cc_start: 0.8158 (p0) cc_final: 0.7845 (p0) REVERT: N 55 LYS cc_start: 0.9221 (mtpp) cc_final: 0.8804 (mtmt) REVERT: N 118 ARG cc_start: 0.6818 (mtp180) cc_final: 0.5648 (mmt-90) REVERT: N 145 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7678 (mm-30) REVERT: P 13 MET cc_start: 0.8402 (mmm) cc_final: 0.7950 (mmm) REVERT: R 28 TRP cc_start: 0.7008 (t-100) cc_final: 0.6503 (t60) REVERT: R 45 ARG cc_start: 0.7937 (mtm180) cc_final: 0.7098 (ttt180) REVERT: R 49 ARG cc_start: 0.7287 (ttm170) cc_final: 0.6912 (ttt-90) REVERT: R 62 ILE cc_start: 0.8491 (tp) cc_final: 0.8146 (mt) REVERT: S 70 LYS cc_start: 0.6960 (tptt) cc_final: 0.6604 (tppt) REVERT: S 73 VAL cc_start: 0.9182 (t) cc_final: 0.8970 (p) REVERT: T 21 LEU cc_start: 0.8688 (mt) cc_final: 0.8116 (tt) REVERT: T 29 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7723 (tpp-160) outliers start: 36 outliers final: 20 residues processed: 430 average time/residue: 0.0964 time to fit residues: 59.4601 Evaluate side-chains 397 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 377 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.141045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111664 restraints weight = 23296.057| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.73 r_work: 0.3433 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12324 Z= 0.189 Angle : 0.684 10.309 16689 Z= 0.338 Chirality : 0.044 0.213 1971 Planarity : 0.004 0.044 2066 Dihedral : 4.187 18.189 1686 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.07 % Allowed : 20.99 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.21), residues: 1558 helix: 1.38 (0.15), residues: 1101 sheet: -0.70 (0.56), residues: 85 loop : -0.81 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 47 TYR 0.016 0.002 TYR S 100 PHE 0.026 0.002 PHE S 64 TRP 0.006 0.001 TRP P 25 HIS 0.003 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00426 (12324) covalent geometry : angle 0.68387 (16689) hydrogen bonds : bond 0.05337 ( 942) hydrogen bonds : angle 4.48351 ( 2796) *********************** 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 449 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 398 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8587 (t) cc_final: 0.8131 (m) REVERT: 5 65 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7430 (tt) REVERT: 6 49 TYR cc_start: 0.7973 (m-10) cc_final: 0.7752 (m-80) REVERT: 7 45 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7734 (tm-30) REVERT: 8 75 MET cc_start: 0.5174 (mmm) cc_final: 0.4779 (mmm) REVERT: 3 1 ASP cc_start: 0.7095 (p0) cc_final: 0.6654 (t70) REVERT: G 104 MET cc_start: 0.7995 (mmt) cc_final: 0.7506 (mmm) REVERT: I 14 ARG cc_start: 0.8158 (tpt90) cc_final: 0.7521 (ttm-80) REVERT: K 26 TYR cc_start: 0.7783 (t80) cc_final: 0.7112 (t80) REVERT: K 87 GLU cc_start: 0.8620 (pp20) cc_final: 0.8280 (pt0) REVERT: M 159 ASN cc_start: 0.8326 (p0) cc_final: 0.8084 (p0) REVERT: N 55 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8824 (mtmt) REVERT: N 118 ARG cc_start: 0.6904 (mtp180) cc_final: 0.5628 (mmt-90) REVERT: N 140 MET cc_start: 0.8241 (pmm) cc_final: 0.7913 (pmm) REVERT: N 145 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7719 (mm-30) REVERT: R 28 TRP cc_start: 0.7028 (t-100) cc_final: 0.6469 (t60) REVERT: R 45 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7098 (ttt180) REVERT: R 49 ARG cc_start: 0.7324 (ttm170) cc_final: 0.6978 (ttt-90) REVERT: R 62 ILE cc_start: 0.8479 (tp) cc_final: 0.8110 (mt) REVERT: S 70 LYS cc_start: 0.6983 (tptt) cc_final: 0.6607 (tppt) REVERT: S 90 GLU cc_start: 0.8339 (tt0) cc_final: 0.7366 (tm-30) REVERT: T 21 LEU cc_start: 0.8720 (mt) cc_final: 0.8136 (tt) REVERT: T 29 ARG cc_start: 0.8061 (ttt180) cc_final: 0.7809 (tpp-160) outliers start: 51 outliers final: 37 residues processed: 420 average time/residue: 0.1041 time to fit residues: 62.6025 Evaluate side-chains 410 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 372 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 65 LEU Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain T residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 81 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.141899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112752 restraints weight = 23077.476| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.69 r_work: 0.3435 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12324 Z= 0.171 Angle : 0.663 9.755 16689 Z= 0.330 Chirality : 0.043 0.231 1971 Planarity : 0.004 0.044 2066 Dihedral : 4.181 17.763 1686 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.63 % Allowed : 21.55 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1558 helix: 1.51 (0.15), residues: 1104 sheet: -0.59 (0.58), residues: 84 loop : -0.64 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 47 TYR 0.019 0.001 TYR 3 49 PHE 0.020 0.002 PHE 7 63 TRP 0.005 0.001 TRP P 25 HIS 0.005 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00375 (12324) covalent geometry : angle 0.66345 (16689) hydrogen bonds : bond 0.05107 ( 942) hydrogen bonds : angle 4.40230 ( 2796) *********************** 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 456 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 398 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.7842 (mttp) cc_final: 0.7603 (mttm) REVERT: 4 48 SER cc_start: 0.8548 (t) cc_final: 0.8080 (m) REVERT: 4 54 PHE cc_start: 0.8107 (t80) cc_final: 0.7657 (t80) REVERT: 5 60 MET cc_start: 0.8041 (mmm) cc_final: 0.7733 (mmm) REVERT: 6 49 TYR cc_start: 0.7929 (m-10) cc_final: 0.7725 (m-80) REVERT: 7 45 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7828 (tm-30) REVERT: 2 47 PHE cc_start: 0.8419 (t80) cc_final: 0.8101 (t80) REVERT: 3 1 ASP cc_start: 0.7052 (p0) cc_final: 0.6692 (t70) REVERT: 3 54 PHE cc_start: 0.8660 (t80) cc_final: 0.8452 (t80) REVERT: 3 58 GLU cc_start: 0.8152 (pp20) cc_final: 0.7812 (tm-30) REVERT: 3 65 LEU cc_start: 0.8662 (mt) cc_final: 0.8437 (tp) REVERT: G 104 MET cc_start: 0.8022 (mmt) cc_final: 0.7535 (mmm) REVERT: G 181 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8326 (tt) REVERT: H 32 ASN cc_start: 0.8382 (m-40) cc_final: 0.7955 (t0) REVERT: H 130 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7712 (tp30) REVERT: I 14 ARG cc_start: 0.8160 (tpt90) cc_final: 0.7542 (ttm-80) REVERT: I 18 ILE cc_start: 0.9014 (mt) cc_final: 0.8469 (mt) REVERT: K 26 TYR cc_start: 0.7784 (t80) cc_final: 0.7019 (t80) REVERT: M 141 GLU cc_start: 0.8777 (pt0) cc_final: 0.8505 (pm20) REVERT: N 22 LEU cc_start: 0.8754 (mp) cc_final: 0.8434 (tt) REVERT: N 55 LYS cc_start: 0.9230 (mtpp) cc_final: 0.8821 (mtmt) REVERT: N 118 ARG cc_start: 0.6973 (mtp180) cc_final: 0.5490 (mmt-90) REVERT: N 140 MET cc_start: 0.8288 (pmm) cc_final: 0.7931 (pmm) REVERT: N 145 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7640 (mm-30) REVERT: R 45 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7118 (ttt180) REVERT: R 49 ARG cc_start: 0.7371 (ttm170) cc_final: 0.6985 (ttt-90) REVERT: S 47 ARG cc_start: 0.8228 (ttp80) cc_final: 0.8000 (ttp80) REVERT: S 50 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8997 (mp10) REVERT: S 68 THR cc_start: 0.7042 (OUTLIER) cc_final: 0.6828 (t) REVERT: S 71 GLU cc_start: 0.8482 (mp0) cc_final: 0.8100 (pm20) REVERT: S 90 GLU cc_start: 0.8376 (tt0) cc_final: 0.7408 (tm-30) REVERT: T 16 TYR cc_start: 0.7298 (m-80) cc_final: 0.7084 (m-10) REVERT: T 21 LEU cc_start: 0.8712 (mt) cc_final: 0.8160 (tt) REVERT: T 29 ARG cc_start: 0.8004 (ttt180) cc_final: 0.7801 (tpp-160) outliers start: 58 outliers final: 34 residues processed: 427 average time/residue: 0.1045 time to fit residues: 64.0413 Evaluate side-chains 414 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 377 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain M residue 125 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain T residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.142504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.113614 restraints weight = 23016.156| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.69 r_work: 0.3452 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12324 Z= 0.156 Angle : 0.665 10.084 16689 Z= 0.330 Chirality : 0.043 0.242 1971 Planarity : 0.004 0.047 2066 Dihedral : 4.158 17.458 1686 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.23 % Allowed : 23.06 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.22), residues: 1558 helix: 1.49 (0.15), residues: 1130 sheet: -0.54 (0.58), residues: 84 loop : -0.22 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 47 TYR 0.021 0.001 TYR 3 49 PHE 0.026 0.002 PHE 7 63 TRP 0.017 0.001 TRP R 28 HIS 0.003 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00344 (12324) covalent geometry : angle 0.66485 (16689) hydrogen bonds : bond 0.04972 ( 942) hydrogen bonds : angle 4.34498 ( 2796) *********************** 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 448 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 395 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8513 (t) cc_final: 0.8070 (m) REVERT: 4 54 PHE cc_start: 0.8085 (t80) cc_final: 0.7740 (t80) REVERT: 6 49 TYR cc_start: 0.7900 (m-10) cc_final: 0.7647 (m-80) REVERT: 8 45 GLN cc_start: 0.6754 (tp40) cc_final: 0.6464 (tp-100) REVERT: 8 66 MET cc_start: 0.7772 (ttp) cc_final: 0.6910 (mmt) REVERT: 3 1 ASP cc_start: 0.6975 (p0) cc_final: 0.6669 (t70) REVERT: 3 58 GLU cc_start: 0.8105 (pp20) cc_final: 0.7832 (tm-30) REVERT: 3 62 LEU cc_start: 0.8528 (mm) cc_final: 0.8061 (mm) REVERT: G 104 MET cc_start: 0.8037 (mmt) cc_final: 0.7594 (mmm) REVERT: G 181 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8263 (tt) REVERT: H 32 ASN cc_start: 0.8390 (m-40) cc_final: 0.7972 (t0) REVERT: H 93 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8469 (mt) REVERT: I 14 ARG cc_start: 0.8151 (tpt90) cc_final: 0.7551 (ttm-80) REVERT: K 26 TYR cc_start: 0.7814 (t80) cc_final: 0.7166 (t80) REVERT: K 84 LYS cc_start: 0.8977 (ttmt) cc_final: 0.7936 (ttpt) REVERT: K 85 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8969 (tt) REVERT: K 88 GLN cc_start: 0.8465 (mp10) cc_final: 0.8079 (mp10) REVERT: M 141 GLU cc_start: 0.8792 (pt0) cc_final: 0.8514 (pm20) REVERT: N 22 LEU cc_start: 0.8749 (mp) cc_final: 0.8431 (tt) REVERT: N 55 LYS cc_start: 0.9247 (mtpp) cc_final: 0.8830 (mtmt) REVERT: N 118 ARG cc_start: 0.7046 (mtp180) cc_final: 0.5701 (mpt180) REVERT: N 145 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7612 (mm-30) REVERT: R 30 LEU cc_start: 0.7887 (pp) cc_final: 0.7487 (mp) REVERT: R 45 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7120 (ttt180) REVERT: R 49 ARG cc_start: 0.7357 (ttm170) cc_final: 0.6981 (ttt-90) REVERT: S 70 LYS cc_start: 0.6922 (tptt) cc_final: 0.6471 (tppt) REVERT: S 90 GLU cc_start: 0.8410 (tt0) cc_final: 0.7424 (tm-30) REVERT: T 21 LEU cc_start: 0.8655 (mt) cc_final: 0.8127 (tt) outliers start: 53 outliers final: 38 residues processed: 421 average time/residue: 0.1137 time to fit residues: 68.0193 Evaluate side-chains 421 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 380 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain T residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN 8 44 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS ** S 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113356 restraints weight = 23076.611| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.70 r_work: 0.3471 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12324 Z= 0.160 Angle : 0.694 12.054 16689 Z= 0.343 Chirality : 0.043 0.265 1971 Planarity : 0.004 0.052 2066 Dihedral : 4.154 17.283 1686 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 4.15 % Allowed : 24.26 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.22), residues: 1558 helix: 1.55 (0.15), residues: 1132 sheet: -0.50 (0.58), residues: 86 loop : -0.24 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 47 TYR 0.021 0.001 TYR N 221 PHE 0.029 0.002 PHE 3 69 TRP 0.017 0.001 TRP R 28 HIS 0.005 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00356 (12324) covalent geometry : angle 0.69392 (16689) hydrogen bonds : bond 0.04930 ( 942) hydrogen bonds : angle 4.34586 ( 2796) *********************** 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 456 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8608 (t) cc_final: 0.8159 (m) REVERT: 6 49 TYR cc_start: 0.7894 (m-10) cc_final: 0.7577 (m-80) REVERT: 8 45 GLN cc_start: 0.6728 (tp40) cc_final: 0.6449 (tp-100) REVERT: 8 66 MET cc_start: 0.7848 (ttp) cc_final: 0.6948 (mmt) REVERT: 3 1 ASP cc_start: 0.6912 (p0) cc_final: 0.6709 (t70) REVERT: 3 58 GLU cc_start: 0.7993 (pp20) cc_final: 0.7697 (tm-30) REVERT: 3 62 LEU cc_start: 0.8595 (mm) cc_final: 0.8122 (mm) REVERT: G 104 MET cc_start: 0.8075 (mmt) cc_final: 0.7686 (mmm) REVERT: G 181 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8198 (tt) REVERT: H 32 ASN cc_start: 0.8401 (m-40) cc_final: 0.8002 (t0) REVERT: H 93 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8469 (mt) REVERT: I 14 ARG cc_start: 0.8037 (tpt90) cc_final: 0.7525 (ttm-80) REVERT: K 26 TYR cc_start: 0.7802 (t80) cc_final: 0.7044 (t80) REVERT: K 84 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8048 (ttpt) REVERT: K 85 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9048 (tt) REVERT: K 88 GLN cc_start: 0.8416 (mp10) cc_final: 0.8067 (mp10) REVERT: M 141 GLU cc_start: 0.8743 (pt0) cc_final: 0.8525 (pm20) REVERT: N 22 LEU cc_start: 0.8816 (mp) cc_final: 0.8503 (tt) REVERT: N 55 LYS cc_start: 0.9237 (mtpp) cc_final: 0.8858 (mtmt) REVERT: N 118 ARG cc_start: 0.7191 (mtp180) cc_final: 0.5797 (mpt180) REVERT: N 140 MET cc_start: 0.8189 (pmm) cc_final: 0.7818 (pmm) REVERT: N 145 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7661 (mm-30) REVERT: N 181 MET cc_start: 0.8623 (mmp) cc_final: 0.8349 (tpp) REVERT: P 39 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.8223 (mtp180) REVERT: R 30 LEU cc_start: 0.7862 (pp) cc_final: 0.7467 (mp) REVERT: R 45 ARG cc_start: 0.7915 (mtm180) cc_final: 0.7096 (ttt180) REVERT: R 49 ARG cc_start: 0.7330 (ttm170) cc_final: 0.6982 (ttt-90) REVERT: S 53 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8800 (mptt) REVERT: S 54 LYS cc_start: 0.9396 (mmmt) cc_final: 0.9081 (tptp) REVERT: S 70 LYS cc_start: 0.6912 (tptt) cc_final: 0.6502 (tppt) REVERT: T 21 LEU cc_start: 0.8576 (mt) cc_final: 0.8078 (tt) REVERT: T 36 ARG cc_start: 0.6279 (ptt180) cc_final: 0.5685 (ptt-90) outliers start: 52 outliers final: 39 residues processed: 425 average time/residue: 0.1020 time to fit residues: 62.1327 Evaluate side-chains 422 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 380 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 4 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 105 optimal weight: 0.0050 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.141394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112526 restraints weight = 22960.677| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.69 r_work: 0.3443 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12324 Z= 0.177 Angle : 0.711 11.361 16689 Z= 0.354 Chirality : 0.045 0.218 1971 Planarity : 0.004 0.056 2066 Dihedral : 4.191 21.217 1686 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.23 % Allowed : 24.66 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.22), residues: 1558 helix: 1.46 (0.15), residues: 1141 sheet: -0.44 (0.58), residues: 86 loop : -0.20 (0.38), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 47 TYR 0.032 0.001 TYR N 221 PHE 0.032 0.002 PHE 3 69 TRP 0.015 0.001 TRP R 28 HIS 0.005 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00400 (12324) covalent geometry : angle 0.71075 (16689) hydrogen bonds : bond 0.04991 ( 942) hydrogen bonds : angle 4.40845 ( 2796) *********************** 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 439 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 386 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 16 VAL cc_start: 0.8092 (t) cc_final: 0.7891 (t) REVERT: 4 48 SER cc_start: 0.8526 (t) cc_final: 0.8061 (m) REVERT: 6 49 TYR cc_start: 0.7968 (m-10) cc_final: 0.7650 (m-80) REVERT: 8 66 MET cc_start: 0.7785 (ttp) cc_final: 0.6883 (mmt) REVERT: 2 47 PHE cc_start: 0.8392 (t80) cc_final: 0.8075 (t80) REVERT: 3 58 GLU cc_start: 0.7939 (pp20) cc_final: 0.7561 (tm-30) REVERT: 3 62 LEU cc_start: 0.8525 (mm) cc_final: 0.8004 (mm) REVERT: G 33 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6306 (ttp80) REVERT: G 104 MET cc_start: 0.8075 (mmt) cc_final: 0.7648 (mmm) REVERT: G 181 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8294 (tt) REVERT: H 32 ASN cc_start: 0.8487 (m-40) cc_final: 0.8071 (t0) REVERT: H 93 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8459 (mt) REVERT: H 130 GLU cc_start: 0.7925 (tp30) cc_final: 0.7701 (tp30) REVERT: I 14 ARG cc_start: 0.8097 (tpt90) cc_final: 0.7543 (ttm-80) REVERT: I 18 ILE cc_start: 0.8901 (mt) cc_final: 0.8628 (mp) REVERT: K 85 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9011 (tt) REVERT: K 88 GLN cc_start: 0.8435 (mp10) cc_final: 0.7982 (mp10) REVERT: M 141 GLU cc_start: 0.8813 (pt0) cc_final: 0.8540 (pm20) REVERT: N 22 LEU cc_start: 0.8785 (mp) cc_final: 0.8436 (tt) REVERT: N 41 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8320 (mtt90) REVERT: N 55 LYS cc_start: 0.9242 (mtpp) cc_final: 0.8831 (mtmt) REVERT: N 118 ARG cc_start: 0.7254 (mtp180) cc_final: 0.5745 (mpt180) REVERT: N 140 MET cc_start: 0.8221 (pmm) cc_final: 0.7593 (pmm) REVERT: N 145 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7647 (mm-30) REVERT: N 181 MET cc_start: 0.8577 (mmp) cc_final: 0.8346 (tpp) REVERT: P 13 MET cc_start: 0.8737 (mmm) cc_final: 0.8371 (mmm) REVERT: R 30 LEU cc_start: 0.7966 (pp) cc_final: 0.7563 (mp) REVERT: R 45 ARG cc_start: 0.8030 (mtm180) cc_final: 0.7159 (ttt180) REVERT: R 49 ARG cc_start: 0.7432 (ttm170) cc_final: 0.7010 (ttt-90) REVERT: R 62 ILE cc_start: 0.8445 (tp) cc_final: 0.8114 (mt) REVERT: S 54 LYS cc_start: 0.9429 (mmmt) cc_final: 0.9133 (tptp) REVERT: T 21 LEU cc_start: 0.8602 (mt) cc_final: 0.8105 (tt) REVERT: T 33 LEU cc_start: 0.9397 (mp) cc_final: 0.9146 (mp) outliers start: 53 outliers final: 37 residues processed: 413 average time/residue: 0.1088 time to fit residues: 63.9486 Evaluate side-chains 417 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain M residue 159 ASN Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 77 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 18 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112616 restraints weight = 23147.890| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.70 r_work: 0.3457 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12324 Z= 0.176 Angle : 0.720 12.276 16689 Z= 0.354 Chirality : 0.045 0.265 1971 Planarity : 0.004 0.055 2066 Dihedral : 4.197 17.938 1686 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.83 % Allowed : 26.18 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.22), residues: 1558 helix: 1.43 (0.15), residues: 1142 sheet: -0.29 (0.58), residues: 84 loop : -0.29 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 47 TYR 0.022 0.002 TYR K 26 PHE 0.035 0.002 PHE 3 69 TRP 0.014 0.001 TRP R 28 HIS 0.003 0.001 HIS R 83 Details of bonding type rmsd covalent geometry : bond 0.00399 (12324) covalent geometry : angle 0.72011 (16689) hydrogen bonds : bond 0.04994 ( 942) hydrogen bonds : angle 4.42694 ( 2796) *********************** 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 433 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 385 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8607 (t) cc_final: 0.8153 (m) REVERT: 6 49 TYR cc_start: 0.7950 (m-10) cc_final: 0.7663 (m-80) REVERT: 8 66 MET cc_start: 0.7881 (ttp) cc_final: 0.6921 (mmt) REVERT: 3 58 GLU cc_start: 0.7959 (pp20) cc_final: 0.7436 (tm-30) REVERT: G 33 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.5992 (ttp80) REVERT: G 36 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.8039 (tmm160) REVERT: G 104 MET cc_start: 0.8106 (mmt) cc_final: 0.7730 (mmm) REVERT: G 181 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8261 (tt) REVERT: H 32 ASN cc_start: 0.8462 (m-40) cc_final: 0.8067 (t0) REVERT: H 93 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8493 (mt) REVERT: I 14 ARG cc_start: 0.8018 (tpt90) cc_final: 0.7499 (ttm-80) REVERT: I 18 ILE cc_start: 0.8917 (mt) cc_final: 0.8649 (mp) REVERT: K 85 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9015 (tt) REVERT: K 88 GLN cc_start: 0.8351 (mp10) cc_final: 0.7970 (mp10) REVERT: M 141 GLU cc_start: 0.8756 (pt0) cc_final: 0.8533 (pm20) REVERT: N 55 LYS cc_start: 0.9234 (mtpp) cc_final: 0.8835 (mtmt) REVERT: N 118 ARG cc_start: 0.7254 (mtp180) cc_final: 0.5744 (mpt180) REVERT: N 140 MET cc_start: 0.8264 (pmm) cc_final: 0.7467 (pmm) REVERT: N 145 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7708 (mm-30) REVERT: N 181 MET cc_start: 0.8605 (mmp) cc_final: 0.8364 (tpp) REVERT: P 13 MET cc_start: 0.8663 (mmm) cc_final: 0.8354 (mmm) REVERT: P 22 GLN cc_start: 0.8574 (pm20) cc_final: 0.8250 (pm20) REVERT: P 28 MET cc_start: 0.8723 (ttm) cc_final: 0.8262 (ttm) REVERT: P 39 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.8376 (mtp180) REVERT: R 30 LEU cc_start: 0.7893 (pp) cc_final: 0.7483 (mp) REVERT: R 45 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7133 (ttt180) REVERT: R 49 ARG cc_start: 0.7403 (ttm170) cc_final: 0.7026 (ttt-90) REVERT: R 62 ILE cc_start: 0.8539 (tp) cc_final: 0.8187 (mt) REVERT: S 54 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9155 (tptp) REVERT: T 21 LEU cc_start: 0.8615 (mt) cc_final: 0.8164 (tt) REVERT: T 34 LYS cc_start: 0.9228 (mmmm) cc_final: 0.8554 (mmmm) outliers start: 48 outliers final: 35 residues processed: 407 average time/residue: 0.1060 time to fit residues: 61.5066 Evaluate side-chains 409 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 370 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 28 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain G residue 33 ARG Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain M residue 159 ASN Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 76 SER Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 77 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 142 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 152 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS 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 = 0.144170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.115669 restraints weight = 22881.874| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.69 r_work: 0.3505 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12324 Z= 0.154 Angle : 0.731 12.726 16689 Z= 0.357 Chirality : 0.045 0.227 1971 Planarity : 0.004 0.071 2066 Dihedral : 4.180 16.983 1686 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.55 % Allowed : 27.93 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.22), residues: 1558 helix: 1.52 (0.15), residues: 1155 sheet: -0.29 (0.58), residues: 84 loop : -0.11 (0.38), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 47 TYR 0.024 0.001 TYR N 221 PHE 0.037 0.002 PHE 3 69 TRP 0.013 0.001 TRP R 28 HIS 0.006 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00337 (12324) covalent geometry : angle 0.73090 (16689) hydrogen bonds : bond 0.04838 ( 942) hydrogen bonds : angle 4.37373 ( 2796) ********************** 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 423 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 391 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8519 (t) cc_final: 0.8055 (m) REVERT: 6 32 LEU cc_start: 0.8340 (tt) cc_final: 0.8100 (tt) REVERT: 6 49 TYR cc_start: 0.7889 (m-10) cc_final: 0.7562 (m-80) REVERT: 8 66 MET cc_start: 0.7845 (ttp) cc_final: 0.6858 (mmt) REVERT: 2 47 PHE cc_start: 0.8334 (t80) cc_final: 0.8034 (t80) REVERT: 3 58 GLU cc_start: 0.7846 (pp20) cc_final: 0.7343 (tm-30) REVERT: G 104 MET cc_start: 0.8094 (mmt) cc_final: 0.7690 (mmm) REVERT: H 32 ASN cc_start: 0.8500 (m-40) cc_final: 0.8071 (t0) REVERT: H 93 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8513 (mt) REVERT: H 128 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7497 (mtt-85) REVERT: I 14 ARG cc_start: 0.8093 (tpt90) cc_final: 0.7720 (tpm170) REVERT: K 85 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8999 (tt) REVERT: K 88 GLN cc_start: 0.8381 (mp10) cc_final: 0.7958 (mp10) REVERT: M 141 GLU cc_start: 0.8779 (pt0) cc_final: 0.8532 (pm20) REVERT: N 55 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8789 (mtmt) REVERT: N 118 ARG cc_start: 0.7278 (mtp180) cc_final: 0.5727 (mpt180) REVERT: N 140 MET cc_start: 0.8305 (pmm) cc_final: 0.7743 (pmm) REVERT: N 145 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7680 (mm-30) REVERT: N 152 GLN cc_start: 0.8807 (mm110) cc_final: 0.8388 (mp10) REVERT: N 181 MET cc_start: 0.8471 (mmp) cc_final: 0.8262 (tpp) REVERT: P 13 MET cc_start: 0.8707 (mmm) cc_final: 0.8332 (mmm) REVERT: P 22 GLN cc_start: 0.8662 (pm20) cc_final: 0.8236 (pm20) REVERT: P 39 ARG cc_start: 0.8833 (mtp-110) cc_final: 0.8470 (mtp180) REVERT: R 30 LEU cc_start: 0.7924 (pp) cc_final: 0.7521 (mp) REVERT: R 45 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7166 (ttt180) REVERT: R 49 ARG cc_start: 0.7340 (ttm170) cc_final: 0.6956 (ttt-90) REVERT: R 62 ILE cc_start: 0.8484 (tp) cc_final: 0.8164 (mt) REVERT: R 88 ARG cc_start: 0.8506 (mtp-110) cc_final: 0.8277 (mtm110) REVERT: S 54 LYS cc_start: 0.9444 (mmmt) cc_final: 0.9195 (tptp) REVERT: S 70 LYS cc_start: 0.8161 (tppt) cc_final: 0.7437 (tppt) REVERT: T 21 LEU cc_start: 0.8672 (mt) cc_final: 0.8236 (tt) REVERT: T 34 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8553 (mmmm) REVERT: T 36 ARG cc_start: 0.6008 (ptt180) cc_final: 0.5565 (ptt-90) REVERT: T 41 ARG cc_start: 0.8622 (mtm180) cc_final: 0.8374 (mtm180) outliers start: 32 outliers final: 22 residues processed: 407 average time/residue: 0.1057 time to fit residues: 60.8575 Evaluate side-chains 401 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 377 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 9 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 4 THR Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain M residue 159 ASN Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 0.0270 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 133 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN ** N 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.145118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.116724 restraints weight = 22821.054| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.70 r_work: 0.3518 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12324 Z= 0.153 Angle : 0.735 13.066 16689 Z= 0.358 Chirality : 0.045 0.228 1971 Planarity : 0.005 0.082 2066 Dihedral : 4.159 16.428 1686 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.39 % Allowed : 28.81 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.22), residues: 1558 helix: 1.58 (0.15), residues: 1152 sheet: -0.26 (0.59), residues: 84 loop : -0.09 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 42 TYR 0.023 0.001 TYR T 32 PHE 0.037 0.002 PHE 3 69 TRP 0.011 0.001 TRP R 28 HIS 0.006 0.001 HIS N 127 Details of bonding type rmsd covalent geometry : bond 0.00335 (12324) covalent geometry : angle 0.73496 (16689) hydrogen bonds : bond 0.04750 ( 942) hydrogen bonds : angle 4.35215 ( 2796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.91 seconds wall clock time: 53 minutes 0.91 seconds (3180.91 seconds total)