Starting phenix.real_space_refine on Wed May 14 14:48:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9q_34577/05_2025/8h9q_34577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9q_34577/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9q_34577/05_2025/8h9q_34577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9q_34577/05_2025/8h9q_34577.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9q_34577/05_2025/8h9q_34577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9q_34577/05_2025/8h9q_34577.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.31, per 1000 atoms: 0.60 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: 3.05 Conformation dependent library (CDL) restraints added in 1.6 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 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: 0.95 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: 3.66 Time building geometry restraints manager: 3.53 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: 21.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 29.290 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (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 TRP 0.005 0.001 TRP N 48 HIS 0.002 0.001 HIS H 51 PHE 0.018 0.001 PHE H 45 TYR 0.016 0.001 TYR G 193 ARG 0.006 0.001 ARG 2 38 Details of bonding type rmsd hydrogen bonds : bond 0.16933 ( 942) hydrogen bonds : angle 7.24291 ( 2796) covalent geometry : bond 0.00520 (12324) covalent geometry : angle 0.73180 (16689) *********************** 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 : 1.345 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: 0.7595 (t0) REVERT: 8 45 GLN cc_start: 0.7416 (tp40) cc_final: 0.7167 (tp40) REVERT: 1 2 ILE cc_start: 0.6704 (tt) cc_final: 0.6476 (tp) REVERT: 2 39 ASN cc_start: 0.8389 (t0) cc_final: 0.7913 (t0) REVERT: 3 62 LEU cc_start: 0.8459 (mt) cc_final: 0.8178 (mt) REVERT: G 104 MET cc_start: 0.7510 (mmt) cc_final: 0.7007 (mmm) REVERT: G 156 ASP cc_start: 0.8075 (t0) cc_final: 0.7591 (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: 0.8197 (m-40) REVERT: H 135 ILE cc_start: 0.8815 (mt) cc_final: 0.8200 (mm) REVERT: H 139 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7765 (mp0) REVERT: I 14 ARG cc_start: 0.7950 (tpt90) cc_final: 0.7522 (ttm-80) REVERT: K 26 TYR cc_start: 0.7554 (t80) cc_final: 0.6722 (t80) REVERT: K 72 LYS cc_start: 0.8633 (mttt) cc_final: 0.8026 (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: 0.7617 (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: 0.8441 (mtmt) REVERT: N 145 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7797 (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: 0.8520 (mp0) REVERT: Q 3 GLN cc_start: 0.9017 (mp10) cc_final: 0.8672 (mp10) REVERT: Q 22 LEU cc_start: 0.9044 (tt) cc_final: 0.8795 (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: 0.6731 (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: 0.6624 (tppt) REVERT: S 90 GLU cc_start: 0.8376 (tt0) cc_final: 0.7499 (tm-30) REVERT: T 16 TYR cc_start: 0.7299 (m-80) cc_final: 0.6897 (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: 0.7695 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.2585 time to fit residues: 195.1362 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 : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.0970 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 35 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116984 restraints weight = 22751.699| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.59 r_work: 0.3522 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12324 Z= 0.168 Angle : 0.691 8.531 16689 Z= 0.344 Chirality : 0.044 0.234 1971 Planarity : 0.004 0.046 2066 Dihedral : 4.164 20.299 1686 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.63 % Allowed : 16.68 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.21), residues: 1558 helix: 0.44 (0.15), residues: 1111 sheet: -1.24 (0.52), residues: 83 loop : -1.32 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 68 HIS 0.004 0.001 HIS R 83 PHE 0.018 0.002 PHE H 45 TYR 0.015 0.002 TYR R 47 ARG 0.006 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.05954 ( 942) hydrogen bonds : angle 4.77604 ( 2796) covalent geometry : bond 0.00340 (12324) covalent geometry : angle 0.69132 (16689) *********************** 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 469 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 436 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 39 ASN cc_start: 0.8250 (t0) cc_final: 0.7925 (t0) REVERT: 2 39 ASN cc_start: 0.8421 (t0) cc_final: 0.8082 (t0) REVERT: G 104 MET cc_start: 0.7795 (mmt) cc_final: 0.7547 (tpt) REVERT: G 125 LEU cc_start: 0.8101 (tp) cc_final: 0.7794 (tp) REVERT: G 222 THR cc_start: 0.7666 (m) cc_final: 0.7424 (m) REVERT: H 136 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8277 (mt-10) REVERT: I 14 ARG cc_start: 0.8023 (tpt90) cc_final: 0.7644 (ttm-80) REVERT: I 18 ILE cc_start: 0.9005 (mt) cc_final: 0.8730 (mm) REVERT: K 26 TYR cc_start: 0.7603 (t80) cc_final: 0.6896 (t80) REVERT: K 72 LYS cc_start: 0.8715 (mttt) cc_final: 0.8098 (mmtt) REVERT: M 128 ASP cc_start: 0.8843 (p0) cc_final: 0.8467 (p0) REVERT: M 159 ASN cc_start: 0.8065 (p0) cc_final: 0.7748 (p0) REVERT: N 55 LYS cc_start: 0.9229 (mtpp) cc_final: 0.8796 (mtmt) REVERT: N 115 MET cc_start: 0.8806 (ppp) cc_final: 0.8597 (ppp) REVERT: N 145 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7799 (mm-30) REVERT: N 152 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8682 (mm-40) REVERT: P 22 GLN cc_start: 0.8280 (pt0) cc_final: 0.8041 (pt0) REVERT: Q 29 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9141 (mm) REVERT: R 28 TRP cc_start: 0.7062 (t-100) cc_final: 0.6627 (t60) REVERT: R 45 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7069 (ttt180) REVERT: R 49 ARG cc_start: 0.7199 (ttm170) cc_final: 0.6869 (ttt-90) REVERT: S 70 LYS cc_start: 0.6862 (tptt) cc_final: 0.6658 (tppt) REVERT: S 90 GLU cc_start: 0.8441 (tt0) cc_final: 0.7451 (tm-30) REVERT: T 29 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7819 (tpp-160) outliers start: 33 outliers final: 14 residues processed: 448 average time/residue: 0.2450 time to fit residues: 156.3185 Evaluate side-chains 405 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 390 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 47 SER 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 63 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 0.0010 chunk 41 optimal weight: 0.9980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 45 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.145300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.116435 restraints weight = 23230.348| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.74 r_work: 0.3498 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12324 Z= 0.151 Angle : 0.652 13.451 16689 Z= 0.321 Chirality : 0.042 0.222 1971 Planarity : 0.004 0.060 2066 Dihedral : 4.076 17.997 1686 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.47 % Allowed : 18.60 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1558 helix: 1.36 (0.16), residues: 1099 sheet: -0.95 (0.60), residues: 71 loop : -0.96 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 25 HIS 0.005 0.001 HIS R 83 PHE 0.020 0.002 PHE 3 54 TYR 0.018 0.001 TYR 3 49 ARG 0.005 0.001 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.05228 ( 942) hydrogen bonds : angle 4.41465 ( 2796) covalent geometry : bond 0.00299 (12324) covalent geometry : angle 0.65155 (16689) *********************** 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 448 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 417 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8606 (t) cc_final: 0.8187 (m) REVERT: 6 49 TYR cc_start: 0.7874 (m-10) cc_final: 0.7657 (m-80) REVERT: 6 60 MET cc_start: 0.7058 (mmm) cc_final: 0.6847 (mmt) REVERT: 8 66 MET cc_start: 0.7765 (ttp) cc_final: 0.6870 (mmt) REVERT: 2 39 ASN cc_start: 0.8372 (t0) cc_final: 0.8009 (t0) REVERT: 3 1 ASP cc_start: 0.7120 (p0) cc_final: 0.6539 (t70) REVERT: G 104 MET cc_start: 0.7845 (mmt) cc_final: 0.7370 (mmm) REVERT: H 136 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8394 (mt-10) REVERT: H 139 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8556 (mt-10) REVERT: I 14 ARG cc_start: 0.8143 (tpt90) cc_final: 0.7726 (ttm-80) REVERT: I 18 ILE cc_start: 0.9033 (mt) cc_final: 0.8721 (mm) REVERT: K 26 TYR cc_start: 0.7624 (t80) cc_final: 0.6862 (t80) REVERT: K 72 LYS cc_start: 0.8630 (mttt) cc_final: 0.7997 (mmtt) REVERT: K 87 GLU cc_start: 0.8664 (pp20) cc_final: 0.8314 (pt0) REVERT: M 159 ASN cc_start: 0.8131 (p0) cc_final: 0.7778 (p0) REVERT: N 55 LYS cc_start: 0.9228 (mtpp) cc_final: 0.8837 (mtpt) REVERT: N 115 MET cc_start: 0.8816 (ppp) cc_final: 0.8490 (ppp) REVERT: N 145 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7685 (mm-30) REVERT: P 13 MET cc_start: 0.8292 (mmm) cc_final: 0.7680 (mmm) REVERT: P 22 GLN cc_start: 0.8352 (pt0) cc_final: 0.8105 (pt0) REVERT: Q 30 ASN cc_start: 0.8743 (t0) cc_final: 0.8528 (t0) REVERT: R 28 TRP cc_start: 0.7095 (t-100) cc_final: 0.6541 (t60) REVERT: R 45 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7117 (ttt180) REVERT: R 49 ARG cc_start: 0.7290 (ttm170) cc_final: 0.6948 (ttt-90) REVERT: S 70 LYS cc_start: 0.6913 (tptt) cc_final: 0.6673 (tppt) REVERT: S 71 GLU cc_start: 0.8516 (mp0) cc_final: 0.8175 (pm20) REVERT: T 21 LEU cc_start: 0.8672 (mt) cc_final: 0.8116 (tt) REVERT: T 29 ARG cc_start: 0.7987 (ttt180) cc_final: 0.7756 (tpp-160) outliers start: 31 outliers final: 16 residues processed: 431 average time/residue: 0.2341 time to fit residues: 143.5705 Evaluate side-chains 401 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 385 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 5 residue 16 VAL 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 3 residue 57 SER Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 44 GLN 3 45 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 = 0.3975 r_free = 0.3975 target = 0.143357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.114096 restraints weight = 22981.948| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.70 r_work: 0.3484 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12324 Z= 0.166 Angle : 0.667 9.820 16689 Z= 0.326 Chirality : 0.042 0.212 1971 Planarity : 0.004 0.045 2066 Dihedral : 4.083 17.425 1686 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.67 % Allowed : 20.75 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1558 helix: 1.41 (0.16), residues: 1123 sheet: -0.59 (0.55), residues: 87 loop : -0.39 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 25 HIS 0.005 0.001 HIS R 83 PHE 0.030 0.002 PHE S 64 TYR 0.018 0.002 TYR 7 49 ARG 0.006 0.000 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.05131 ( 942) hydrogen bonds : angle 4.37537 ( 2796) covalent geometry : bond 0.00366 (12324) covalent geometry : angle 0.66730 (16689) *********************** 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 445 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 399 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.8032 (mttm) cc_final: 0.7719 (mttm) REVERT: 4 48 SER cc_start: 0.8605 (t) cc_final: 0.8168 (m) REVERT: 5 65 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7387 (tt) REVERT: 6 49 TYR cc_start: 0.7892 (m-10) cc_final: 0.7656 (m-80) REVERT: 6 60 MET cc_start: 0.7042 (mmm) cc_final: 0.6816 (mmt) REVERT: 7 45 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7730 (tm-30) REVERT: 7 58 GLU cc_start: 0.8183 (tt0) cc_final: 0.7877 (tp30) REVERT: 8 66 MET cc_start: 0.7791 (ttp) cc_final: 0.6884 (mmt) REVERT: 1 58 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7513 (tm-30) REVERT: 2 39 ASN cc_start: 0.8424 (t0) cc_final: 0.8078 (t0) REVERT: 3 1 ASP cc_start: 0.7066 (p0) cc_final: 0.6611 (t70) REVERT: G 104 MET cc_start: 0.7944 (mmt) cc_final: 0.7489 (mmm) REVERT: H 136 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8358 (mt-10) REVERT: H 139 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8473 (mt-10) REVERT: I 14 ARG cc_start: 0.8132 (tpt90) cc_final: 0.7477 (ttm-80) REVERT: I 18 ILE cc_start: 0.9047 (mt) cc_final: 0.8693 (mp) REVERT: K 26 TYR cc_start: 0.7703 (t80) cc_final: 0.7012 (t80) REVERT: K 87 GLU cc_start: 0.8598 (pp20) cc_final: 0.8288 (pt0) REVERT: M 159 ASN cc_start: 0.8210 (p0) cc_final: 0.7939 (p0) REVERT: N 55 LYS cc_start: 0.9234 (mtpp) cc_final: 0.8845 (mtpt) REVERT: N 115 MET cc_start: 0.8827 (ppp) cc_final: 0.8477 (ppp) REVERT: N 118 ARG cc_start: 0.6811 (mtp180) cc_final: 0.5674 (mmt-90) REVERT: N 140 MET cc_start: 0.8304 (pmm) cc_final: 0.7961 (pmm) REVERT: N 145 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7669 (mm-30) REVERT: P 13 MET cc_start: 0.8456 (mmm) cc_final: 0.7924 (mmm) REVERT: R 28 TRP cc_start: 0.7011 (t-100) cc_final: 0.6378 (t60) REVERT: R 45 ARG cc_start: 0.7945 (mtm180) cc_final: 0.7117 (ttt180) REVERT: R 49 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6947 (ttt-90) REVERT: R 62 ILE cc_start: 0.8439 (tp) cc_final: 0.8120 (mt) REVERT: S 70 LYS cc_start: 0.6914 (tptt) cc_final: 0.6699 (tppt) REVERT: S 71 GLU cc_start: 0.8434 (mp0) cc_final: 0.8118 (pm20) REVERT: S 90 GLU cc_start: 0.8340 (tt0) cc_final: 0.7421 (tm-30) REVERT: T 21 LEU cc_start: 0.8711 (mt) cc_final: 0.8118 (tt) outliers start: 46 outliers final: 28 residues processed: 419 average time/residue: 0.2439 time to fit residues: 144.5342 Evaluate side-chains 411 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 382 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 58 GLU 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 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 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 3 residue 57 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain H residue 81 SER 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 N residue 39 ASN Chi-restraints excluded: chain Q residue 19 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 15 optimal weight: 0.7980 chunk 101 optimal weight: 0.0010 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN ** N 127 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 = 0.4007 r_free = 0.4007 target = 0.146033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.117194 restraints weight = 22931.497| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.64 r_work: 0.3505 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12324 Z= 0.140 Angle : 0.650 10.118 16689 Z= 0.317 Chirality : 0.042 0.231 1971 Planarity : 0.004 0.046 2066 Dihedral : 4.082 16.638 1686 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.27 % Allowed : 22.43 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1558 helix: 1.55 (0.16), residues: 1126 sheet: -0.43 (0.57), residues: 86 loop : -0.21 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 25 HIS 0.005 0.001 HIS R 83 PHE 0.021 0.001 PHE 7 63 TYR 0.023 0.001 TYR 2 49 ARG 0.010 0.001 ARG S 47 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 942) hydrogen bonds : angle 4.27480 ( 2796) covalent geometry : bond 0.00295 (12324) covalent geometry : angle 0.64982 (16689) *********************** 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 446 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 405 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.8006 (mttm) cc_final: 0.7750 (mttm) REVERT: 4 48 SER cc_start: 0.8659 (t) cc_final: 0.8227 (m) REVERT: 6 32 LEU cc_start: 0.8512 (tt) cc_final: 0.8280 (tt) REVERT: 6 49 TYR cc_start: 0.7757 (m-10) cc_final: 0.7518 (m-80) REVERT: 6 60 MET cc_start: 0.7009 (mmm) cc_final: 0.6723 (mmt) REVERT: 7 58 GLU cc_start: 0.8217 (tt0) cc_final: 0.7772 (tp30) REVERT: 8 45 GLN cc_start: 0.6752 (tp40) cc_final: 0.6460 (tp-100) REVERT: 8 66 MET cc_start: 0.7851 (ttp) cc_final: 0.6886 (mmt) REVERT: 2 39 ASN cc_start: 0.8354 (t0) cc_final: 0.8079 (t0) REVERT: 3 1 ASP cc_start: 0.7050 (p0) cc_final: 0.6593 (t70) REVERT: G 36 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7897 (ttp80) REVERT: G 104 MET cc_start: 0.7969 (mmt) cc_final: 0.7484 (mmm) REVERT: H 132 GLN cc_start: 0.9135 (tp-100) cc_final: 0.8863 (tp-100) REVERT: H 136 GLU cc_start: 0.8711 (mt-10) cc_final: 0.7984 (mt-10) REVERT: H 139 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8061 (mp0) REVERT: I 13 ILE cc_start: 0.8973 (mm) cc_final: 0.8577 (mm) REVERT: I 14 ARG cc_start: 0.8062 (tpt90) cc_final: 0.7462 (ttm-80) REVERT: I 18 ILE cc_start: 0.9024 (mt) cc_final: 0.8673 (mp) REVERT: K 26 TYR cc_start: 0.7667 (t80) cc_final: 0.6904 (t80) REVERT: M 159 ASN cc_start: 0.8184 (p0) cc_final: 0.7926 (p0) REVERT: N 55 LYS cc_start: 0.9231 (mtpp) cc_final: 0.8864 (mtpt) REVERT: N 115 MET cc_start: 0.8737 (ppp) cc_final: 0.8412 (ppp) REVERT: N 118 ARG cc_start: 0.6905 (mtp180) cc_final: 0.5626 (mmt-90) REVERT: N 145 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7685 (mm-30) REVERT: P 13 MET cc_start: 0.8267 (mmm) cc_final: 0.7909 (mmm) REVERT: R 45 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7114 (ttt180) REVERT: R 49 ARG cc_start: 0.7273 (ttm170) cc_final: 0.6918 (ttt-90) REVERT: R 62 ILE cc_start: 0.8443 (tp) cc_final: 0.8135 (mt) REVERT: S 54 LYS cc_start: 0.9410 (mmmt) cc_final: 0.8996 (tptp) REVERT: S 70 LYS cc_start: 0.6908 (tptt) cc_final: 0.6623 (tppt) REVERT: S 71 GLU cc_start: 0.8407 (mp0) cc_final: 0.8059 (pm20) REVERT: S 90 GLU cc_start: 0.8356 (tt0) cc_final: 0.7441 (tm-30) REVERT: T 21 LEU cc_start: 0.8648 (mt) cc_final: 0.8111 (tt) REVERT: T 36 ARG cc_start: 0.6042 (ptt180) cc_final: 0.5267 (ptt-90) outliers start: 41 outliers final: 23 residues processed: 421 average time/residue: 0.2378 time to fit residues: 141.0269 Evaluate side-chains 405 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 382 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 66 MET 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 65 LEU Chi-restraints excluded: chain 1 residue 18 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 G residue 168 VAL Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 43 LEU 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 Q residue 26 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 6 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 0.0030 chunk 117 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN ** 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 = 0.3928 r_free = 0.3928 target = 0.139812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110514 restraints weight = 23639.057| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.64 r_work: 0.3425 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12324 Z= 0.236 Angle : 0.724 9.494 16689 Z= 0.361 Chirality : 0.045 0.207 1971 Planarity : 0.004 0.048 2066 Dihedral : 4.185 17.426 1686 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.71 % Allowed : 22.98 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1558 helix: 1.29 (0.15), residues: 1136 sheet: -0.48 (0.58), residues: 86 loop : -0.21 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.032 0.002 PHE 7 63 TYR 0.025 0.002 TYR 3 49 ARG 0.007 0.001 ARG R 88 Details of bonding type rmsd hydrogen bonds : bond 0.05265 ( 942) hydrogen bonds : angle 4.52022 ( 2796) covalent geometry : bond 0.00537 (12324) covalent geometry : angle 0.72447 (16689) *********************** 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 446 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 387 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8650 (t) cc_final: 0.8195 (m) REVERT: 6 60 MET cc_start: 0.7085 (mmm) cc_final: 0.6724 (mmt) REVERT: 7 58 GLU cc_start: 0.8327 (tt0) cc_final: 0.7873 (tp30) REVERT: 8 45 GLN cc_start: 0.6842 (tp40) cc_final: 0.6602 (tp40) REVERT: 8 66 MET cc_start: 0.7887 (ttp) cc_final: 0.6949 (mmt) REVERT: 2 39 ASN cc_start: 0.8532 (t0) cc_final: 0.8239 (t0) REVERT: 3 1 ASP cc_start: 0.7023 (p0) cc_final: 0.6716 (t70) REVERT: 3 60 MET cc_start: 0.7290 (mtm) cc_final: 0.6890 (mtp) REVERT: G 104 MET cc_start: 0.8059 (mmt) cc_final: 0.7595 (mmm) REVERT: G 181 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8342 (tt) REVERT: H 32 ASN cc_start: 0.8398 (m-40) cc_final: 0.8015 (t0) REVERT: H 132 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8900 (tp-100) REVERT: H 135 ILE cc_start: 0.8810 (mm) cc_final: 0.7749 (mm) REVERT: H 136 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8059 (mt-10) REVERT: H 139 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8146 (mp0) REVERT: I 14 ARG cc_start: 0.8177 (tpt90) cc_final: 0.7676 (ttm-80) REVERT: K 26 TYR cc_start: 0.7808 (t80) cc_final: 0.7130 (t80) REVERT: K 84 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8240 (ttpt) REVERT: K 85 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9083 (tt) REVERT: K 88 GLN cc_start: 0.8494 (mp10) cc_final: 0.8229 (mp10) REVERT: N 22 LEU cc_start: 0.8824 (mp) cc_final: 0.8503 (tt) REVERT: N 55 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8842 (mtmt) REVERT: N 118 ARG cc_start: 0.7047 (mtp180) cc_final: 0.5706 (mmt-90) REVERT: N 140 MET cc_start: 0.8248 (pmm) cc_final: 0.7906 (pmm) REVERT: N 145 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7745 (mm-30) REVERT: R 30 LEU cc_start: 0.7896 (pp) cc_final: 0.7498 (mp) REVERT: R 45 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7098 (ttt180) REVERT: R 49 ARG cc_start: 0.7416 (ttm170) cc_final: 0.6958 (ttt-90) REVERT: T 21 LEU cc_start: 0.8656 (mt) cc_final: 0.8110 (tt) outliers start: 59 outliers final: 39 residues processed: 418 average time/residue: 0.2422 time to fit residues: 143.6444 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 : 1.352 ------------------------------------------------------------------------------- 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 4 residue 66 MET Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 6 residue 67 VAL Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 7 residue 62 LEU Chi-restraints excluded: chain 8 residue 33 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 64 CYS Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 62 LEU 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 75 MET Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain G residue 146 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 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 M residue 125 ILE Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 116 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 3 45 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113056 restraints weight = 23150.334| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.75 r_work: 0.3454 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12324 Z= 0.157 Angle : 0.684 11.840 16689 Z= 0.339 Chirality : 0.043 0.219 1971 Planarity : 0.004 0.050 2066 Dihedral : 4.159 17.771 1686 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.67 % Allowed : 25.14 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.22), residues: 1558 helix: 1.52 (0.15), residues: 1130 sheet: -0.42 (0.58), residues: 86 loop : -0.21 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.037 0.002 PHE 4 54 TYR 0.022 0.002 TYR 3 49 ARG 0.010 0.001 ARG S 47 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 942) hydrogen bonds : angle 4.35697 ( 2796) covalent geometry : bond 0.00346 (12324) covalent geometry : angle 0.68447 (16689) *********************** 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 449 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8511 (t) cc_final: 0.8053 (m) REVERT: 6 60 MET cc_start: 0.6831 (mmm) cc_final: 0.6606 (mmt) REVERT: 7 45 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7873 (tm-30) REVERT: 7 58 GLU cc_start: 0.8264 (tt0) cc_final: 0.7753 (tp30) REVERT: 8 45 GLN cc_start: 0.6832 (tp40) cc_final: 0.6511 (tp-100) REVERT: 8 66 MET cc_start: 0.7846 (ttp) cc_final: 0.6905 (mmt) REVERT: 2 39 ASN cc_start: 0.8429 (t0) cc_final: 0.8118 (t0) REVERT: 2 75 MET cc_start: 0.6451 (mmm) cc_final: 0.5945 (mmt) REVERT: 3 58 GLU cc_start: 0.7961 (pp20) cc_final: 0.7434 (tm-30) REVERT: 3 60 MET cc_start: 0.7248 (mtm) cc_final: 0.6873 (mtp) REVERT: G 36 ARG cc_start: 0.8324 (ttp80) cc_final: 0.7977 (ttp80) REVERT: G 104 MET cc_start: 0.8038 (mmt) cc_final: 0.7579 (mmm) REVERT: G 181 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8275 (tt) REVERT: H 32 ASN cc_start: 0.8442 (m-40) cc_final: 0.8002 (t0) REVERT: H 132 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8888 (tp-100) REVERT: H 135 ILE cc_start: 0.8809 (mm) cc_final: 0.7815 (mm) REVERT: H 136 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8076 (mt-10) REVERT: H 139 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8132 (mp0) REVERT: I 14 ARG cc_start: 0.8184 (tpt90) cc_final: 0.7629 (ttm-80) REVERT: I 18 ILE cc_start: 0.9002 (mt) cc_final: 0.8638 (mp) REVERT: K 13 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8251 (mtp85) REVERT: K 26 TYR cc_start: 0.7779 (t80) cc_final: 0.7043 (t80) REVERT: K 84 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8006 (ttpt) REVERT: K 85 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9014 (tt) REVERT: K 88 GLN cc_start: 0.8449 (mp10) cc_final: 0.8019 (mp10) REVERT: N 22 LEU cc_start: 0.8756 (mp) cc_final: 0.8436 (tt) REVERT: N 55 LYS cc_start: 0.9241 (mtpp) cc_final: 0.8834 (mtmt) REVERT: N 100 MET cc_start: 0.8277 (ttp) cc_final: 0.8037 (ttp) REVERT: N 118 ARG cc_start: 0.7039 (mtp180) cc_final: 0.5634 (mmt-90) REVERT: N 140 MET cc_start: 0.8227 (pmm) cc_final: 0.7924 (pmm) REVERT: N 145 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7748 (mm-30) REVERT: P 13 MET cc_start: 0.8475 (mmm) cc_final: 0.7868 (mmm) REVERT: R 30 LEU cc_start: 0.7908 (pp) cc_final: 0.7537 (mp) REVERT: R 45 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7139 (ttt180) REVERT: R 49 ARG cc_start: 0.7383 (ttm170) cc_final: 0.6994 (ttt-90) REVERT: S 70 LYS cc_start: 0.7267 (tptt) cc_final: 0.6968 (tppt) REVERT: S 90 GLU cc_start: 0.8383 (tt0) cc_final: 0.7418 (tm-30) REVERT: T 21 LEU cc_start: 0.8657 (mt) cc_final: 0.8143 (tt) REVERT: T 41 ARG cc_start: 0.8651 (mtm180) cc_final: 0.8251 (mtm180) outliers start: 46 outliers final: 30 residues processed: 425 average time/residue: 0.2399 time to fit residues: 143.6944 Evaluate side-chains 412 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 380 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 4 residue 66 MET 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 65 LEU Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 71 ILE Chi-restraints excluded: chain 2 residue 72 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 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 Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 124 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 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 = 0.3959 r_free = 0.3959 target = 0.142065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113005 restraints weight = 23265.043| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.73 r_work: 0.3446 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12324 Z= 0.172 Angle : 0.705 11.093 16689 Z= 0.349 Chirality : 0.044 0.250 1971 Planarity : 0.004 0.053 2066 Dihedral : 4.181 20.692 1686 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.83 % Allowed : 25.30 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1558 helix: 1.45 (0.15), residues: 1140 sheet: -0.43 (0.58), residues: 86 loop : -0.11 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.031 0.002 PHE 3 69 TYR 0.033 0.002 TYR N 221 ARG 0.009 0.001 ARG S 47 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 942) hydrogen bonds : angle 4.38526 ( 2796) covalent geometry : bond 0.00388 (12324) covalent geometry : angle 0.70478 (16689) *********************** 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 441 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 393 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 16 VAL cc_start: 0.8048 (t) cc_final: 0.7846 (t) REVERT: 4 48 SER cc_start: 0.8532 (t) cc_final: 0.8053 (m) REVERT: 6 49 TYR cc_start: 0.7836 (m-80) cc_final: 0.7527 (m-80) REVERT: 7 45 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7851 (tm-30) REVERT: 7 58 GLU cc_start: 0.8280 (tt0) cc_final: 0.7843 (tp30) REVERT: 8 66 MET cc_start: 0.7848 (ttp) cc_final: 0.6900 (mmt) REVERT: 2 39 ASN cc_start: 0.8415 (t0) cc_final: 0.8143 (t0) REVERT: G 104 MET cc_start: 0.8084 (mmt) cc_final: 0.7663 (mmm) REVERT: G 181 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8280 (tt) REVERT: H 32 ASN cc_start: 0.8426 (m-40) cc_final: 0.8015 (t0) REVERT: H 93 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8477 (mt) REVERT: H 109 LYS cc_start: 0.8902 (tptp) cc_final: 0.8638 (mtpt) REVERT: H 132 GLN cc_start: 0.9135 (tp-100) cc_final: 0.8843 (tp-100) REVERT: H 135 ILE cc_start: 0.8819 (mm) cc_final: 0.7789 (mm) REVERT: H 136 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8060 (mt-10) REVERT: H 139 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8124 (mp0) REVERT: I 14 ARG cc_start: 0.8202 (tpt90) cc_final: 0.7731 (ttm-80) REVERT: K 26 TYR cc_start: 0.7779 (t80) cc_final: 0.6995 (t80) REVERT: K 85 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9001 (tt) REVERT: K 88 GLN cc_start: 0.8421 (mp10) cc_final: 0.7995 (mp10) REVERT: M 141 GLU cc_start: 0.8836 (pt0) cc_final: 0.8519 (pm20) REVERT: N 22 LEU cc_start: 0.8765 (mp) cc_final: 0.8423 (tt) REVERT: N 41 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8313 (mtt90) REVERT: N 55 LYS cc_start: 0.9248 (mtpp) cc_final: 0.8832 (mtmt) REVERT: N 118 ARG cc_start: 0.7211 (mtp180) cc_final: 0.5627 (mmt-90) REVERT: N 140 MET cc_start: 0.8243 (pmm) cc_final: 0.7880 (pmm) REVERT: N 145 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7731 (mm-30) REVERT: P 13 MET cc_start: 0.8516 (mmm) cc_final: 0.7917 (mmm) REVERT: P 39 ARG cc_start: 0.8815 (mtp-110) cc_final: 0.8383 (mtp180) REVERT: R 20 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8120 (p) REVERT: R 30 LEU cc_start: 0.7899 (pp) cc_final: 0.7523 (mp) REVERT: R 45 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7141 (ttt180) REVERT: R 49 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6953 (ttt-90) REVERT: S 54 LYS cc_start: 0.9431 (OUTLIER) cc_final: 0.9124 (tptp) REVERT: S 90 GLU cc_start: 0.8406 (tt0) cc_final: 0.7403 (tm-30) REVERT: T 21 LEU cc_start: 0.8623 (mt) cc_final: 0.8141 (tt) outliers start: 48 outliers final: 32 residues processed: 416 average time/residue: 0.2479 time to fit residues: 145.5049 Evaluate side-chains 413 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 376 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 4 residue 66 MET 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 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 2 residue 60 MET Chi-restraints excluded: chain 3 residue 41 SER 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 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 Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 20 VAL 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 54 LYS 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 11 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 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 = 0.3963 r_free = 0.3963 target = 0.142926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.114294 restraints weight = 22944.409| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.72 r_work: 0.3457 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12324 Z= 0.159 Angle : 0.743 13.800 16689 Z= 0.364 Chirality : 0.046 0.362 1971 Planarity : 0.004 0.056 2066 Dihedral : 4.184 18.875 1686 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.75 % Allowed : 26.02 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.22), residues: 1558 helix: 1.48 (0.15), residues: 1142 sheet: -0.25 (0.59), residues: 84 loop : -0.16 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 28 HIS 0.005 0.001 HIS R 83 PHE 0.031 0.002 PHE 4 54 TYR 0.023 0.002 TYR K 44 ARG 0.009 0.001 ARG S 47 Details of bonding type rmsd hydrogen bonds : bond 0.04980 ( 942) hydrogen bonds : angle 4.36089 ( 2796) covalent geometry : bond 0.00353 (12324) covalent geometry : angle 0.74330 (16689) *********************** 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 447 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 400 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8532 (t) cc_final: 0.8049 (m) REVERT: 6 45 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6382 (tp40) REVERT: 6 49 TYR cc_start: 0.7834 (m-80) cc_final: 0.7397 (m-80) REVERT: 6 60 MET cc_start: 0.6814 (mmm) cc_final: 0.6164 (mmm) REVERT: 7 58 GLU cc_start: 0.8238 (tt0) cc_final: 0.7959 (tp30) REVERT: 8 66 MET cc_start: 0.7886 (ttp) cc_final: 0.6921 (mmt) REVERT: 2 39 ASN cc_start: 0.8357 (t0) cc_final: 0.8078 (t0) REVERT: G 104 MET cc_start: 0.8065 (mmt) cc_final: 0.7648 (mmm) REVERT: G 181 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8218 (tt) REVERT: H 32 ASN cc_start: 0.8412 (m-40) cc_final: 0.7982 (t0) REVERT: H 93 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8509 (mt) REVERT: H 135 ILE cc_start: 0.8904 (mm) cc_final: 0.7857 (mm) REVERT: H 139 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8122 (mp0) REVERT: I 14 ARG cc_start: 0.8152 (tpt90) cc_final: 0.7664 (ttm-80) REVERT: I 18 ILE cc_start: 0.8916 (mt) cc_final: 0.8632 (mp) REVERT: K 7 GLU cc_start: 0.7772 (tt0) cc_final: 0.7314 (tp30) REVERT: K 26 TYR cc_start: 0.7763 (t80) cc_final: 0.6974 (t80) REVERT: M 141 GLU cc_start: 0.8853 (pt0) cc_final: 0.8558 (pm20) REVERT: N 22 LEU cc_start: 0.8774 (mp) cc_final: 0.8413 (tt) REVERT: N 41 ARG cc_start: 0.8567 (mtt180) cc_final: 0.8291 (mtt90) REVERT: N 55 LYS cc_start: 0.9247 (mtpp) cc_final: 0.8833 (mtmt) REVERT: N 118 ARG cc_start: 0.7255 (mtp180) cc_final: 0.5655 (mmt-90) REVERT: N 140 MET cc_start: 0.8320 (pmm) cc_final: 0.7814 (pmm) REVERT: N 145 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7677 (mm-30) REVERT: P 13 MET cc_start: 0.8465 (mmm) cc_final: 0.7835 (mmm) REVERT: P 39 ARG cc_start: 0.8814 (mtp-110) cc_final: 0.8398 (mtp180) REVERT: R 20 VAL cc_start: 0.8238 (OUTLIER) cc_final: 0.8030 (p) REVERT: R 30 LEU cc_start: 0.7905 (pp) cc_final: 0.7534 (mp) REVERT: R 45 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7152 (ttt180) REVERT: R 49 ARG cc_start: 0.7410 (ttm170) cc_final: 0.7006 (ttt-90) REVERT: S 54 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9159 (tptp) REVERT: S 77 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8102 (pp) REVERT: S 90 GLU cc_start: 0.8407 (tt0) cc_final: 0.7465 (tm-30) REVERT: T 21 LEU cc_start: 0.8645 (mt) cc_final: 0.8195 (tt) outliers start: 47 outliers final: 32 residues processed: 419 average time/residue: 0.2365 time to fit residues: 140.0101 Evaluate side-chains 421 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 383 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 69 PHE Chi-restraints excluded: chain 6 residue 45 GLN Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 60 MET Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 57 SER 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 87 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 65 ILE 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 54 LYS Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain T residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 62 optimal weight: 0.0060 chunk 75 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 127 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115406 restraints weight = 22881.555| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.74 r_work: 0.3483 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12324 Z= 0.155 Angle : 0.781 23.612 16689 Z= 0.372 Chirality : 0.046 0.338 1971 Planarity : 0.004 0.056 2066 Dihedral : 4.210 18.202 1686 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.95 % Allowed : 27.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.22), residues: 1558 helix: 1.49 (0.15), residues: 1141 sheet: -0.24 (0.59), residues: 84 loop : -0.15 (0.37), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.006 0.001 HIS N 127 PHE 0.043 0.002 PHE 4 54 TYR 0.028 0.002 TYR T 32 ARG 0.010 0.001 ARG S 47 Details of bonding type rmsd hydrogen bonds : bond 0.04911 ( 942) hydrogen bonds : angle 4.38489 ( 2796) covalent geometry : bond 0.00336 (12324) covalent geometry : angle 0.78068 (16689) ********************** 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 426 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 389 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8577 (t) cc_final: 0.8083 (m) REVERT: 6 49 TYR cc_start: 0.7758 (m-80) cc_final: 0.7400 (m-80) REVERT: 6 60 MET cc_start: 0.6743 (mmm) cc_final: 0.6121 (mmm) REVERT: 7 45 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7700 (tm-30) REVERT: 7 58 GLU cc_start: 0.8207 (tt0) cc_final: 0.7938 (tp30) REVERT: 8 66 MET cc_start: 0.7892 (ttp) cc_final: 0.6883 (mmt) REVERT: 2 39 ASN cc_start: 0.8312 (t0) cc_final: 0.8021 (t0) REVERT: G 104 MET cc_start: 0.8069 (mmt) cc_final: 0.7651 (mmm) REVERT: H 32 ASN cc_start: 0.8441 (m-40) cc_final: 0.8018 (t0) REVERT: H 93 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8524 (mt) REVERT: H 130 GLU cc_start: 0.8009 (tp30) cc_final: 0.7808 (tp30) REVERT: H 135 ILE cc_start: 0.8884 (mm) cc_final: 0.7836 (mm) REVERT: H 139 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8130 (mp0) REVERT: I 14 ARG cc_start: 0.8152 (tpt90) cc_final: 0.7843 (ttm-80) REVERT: K 26 TYR cc_start: 0.7760 (t80) cc_final: 0.6912 (t80) REVERT: K 84 LYS cc_start: 0.9018 (ttmt) cc_final: 0.7944 (ttpt) REVERT: K 88 GLN cc_start: 0.8435 (mp10) cc_final: 0.8015 (mp10) REVERT: M 141 GLU cc_start: 0.8826 (pt0) cc_final: 0.8533 (pm20) REVERT: N 22 LEU cc_start: 0.8763 (mp) cc_final: 0.8394 (tt) REVERT: N 41 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8276 (mtt90) REVERT: N 55 LYS cc_start: 0.9218 (mtpp) cc_final: 0.8801 (mtmt) REVERT: N 118 ARG cc_start: 0.7227 (mtp180) cc_final: 0.5613 (mmt-90) REVERT: N 140 MET cc_start: 0.8406 (pmm) cc_final: 0.7924 (pmm) REVERT: N 145 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7618 (mm-30) REVERT: N 152 GLN cc_start: 0.8764 (mm110) cc_final: 0.8336 (mp10) REVERT: P 13 MET cc_start: 0.8427 (mmm) cc_final: 0.7761 (mmm) REVERT: P 39 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.8374 (mtp180) REVERT: R 30 LEU cc_start: 0.7894 (pp) cc_final: 0.7522 (mp) REVERT: R 45 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7162 (ttt180) REVERT: R 49 ARG cc_start: 0.7361 (ttm170) cc_final: 0.7001 (ttt-90) REVERT: S 54 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.9176 (tptp) REVERT: S 77 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8076 (pp) REVERT: S 90 GLU cc_start: 0.8387 (tt0) cc_final: 0.7461 (tm-30) REVERT: T 21 LEU cc_start: 0.8686 (mt) cc_final: 0.8237 (tt) outliers start: 37 outliers final: 28 residues processed: 403 average time/residue: 0.2360 time to fit residues: 134.6849 Evaluate side-chains 406 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 375 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 28 VAL 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 65 LEU Chi-restraints excluded: chain 1 residue 32 LEU Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 57 SER Chi-restraints excluded: chain 3 residue 64 CYS Chi-restraints excluded: chain G residue 168 VAL 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 87 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 54 LYS 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 39 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 104 optimal weight: 0.0070 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 107 optimal weight: 0.0270 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.146634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.119174 restraints weight = 22795.345| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.60 r_work: 0.3530 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12324 Z= 0.160 Angle : 0.777 20.625 16689 Z= 0.370 Chirality : 0.046 0.339 1971 Planarity : 0.004 0.058 2066 Dihedral : 4.203 16.929 1686 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.87 % Allowed : 27.69 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1558 helix: 1.47 (0.15), residues: 1156 sheet: -0.19 (0.58), residues: 84 loop : -0.08 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.006 0.001 HIS N 127 PHE 0.057 0.002 PHE 4 54 TYR 0.022 0.001 TYR K 44 ARG 0.010 0.001 ARG S 47 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 942) hydrogen bonds : angle 4.37596 ( 2796) covalent geometry : bond 0.00354 (12324) covalent geometry : angle 0.77732 (16689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6369.66 seconds wall clock time: 111 minutes 52.08 seconds (6712.08 seconds total)