Starting phenix.real_space_refine on Sat Nov 16 20:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/11_2024/8h9q_34577.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/11_2024/8h9q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/11_2024/8h9q_34577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/11_2024/8h9q_34577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/11_2024/8h9q_34577.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9q_34577/11_2024/8h9q_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-5513/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: 9.47, per 1000 atoms: 0.78 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 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: 1.03 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: 3.89 Time building geometry restraints manager: 3.89 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: 8.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.390 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.200 ------------------------------------------------------------------------------- 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= 0.338 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 *********************** 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 : 1.321 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: 0.2787 time to fit residues: 209.0947 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 : 1.264 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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= 0.223 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 *********************** 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 : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 39 ASN cc_start: 0.8019 (t0) cc_final: 0.7571 (t0) REVERT: 8 45 GLN cc_start: 0.7133 (tp40) cc_final: 0.6848 (tp-100) REVERT: 2 39 ASN cc_start: 0.8215 (t0) cc_final: 0.7738 (t0) REVERT: G 104 MET cc_start: 0.7524 (mmt) cc_final: 0.7234 (tpt) REVERT: G 125 LEU cc_start: 0.7969 (tp) cc_final: 0.7612 (tp) REVERT: G 202 GLN cc_start: 0.8297 (tt0) cc_final: 0.8096 (tt0) REVERT: G 222 THR cc_start: 0.7442 (m) cc_final: 0.7221 (m) REVERT: H 136 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8277 (mt-10) REVERT: I 14 ARG cc_start: 0.8097 (tpt90) cc_final: 0.7677 (ttm-80) REVERT: I 18 ILE cc_start: 0.9000 (mt) cc_final: 0.8709 (mm) REVERT: K 26 TYR cc_start: 0.7490 (t80) cc_final: 0.6795 (t80) REVERT: K 72 LYS cc_start: 0.8593 (mttt) cc_final: 0.7987 (mmtt) REVERT: M 128 ASP cc_start: 0.8731 (p0) cc_final: 0.8368 (p0) REVERT: M 159 ASN cc_start: 0.8044 (p0) cc_final: 0.7790 (p0) REVERT: N 55 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8546 (mtmt) REVERT: N 115 MET cc_start: 0.8836 (ppp) cc_final: 0.8598 (ppp) REVERT: N 145 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7759 (mm-30) REVERT: N 152 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8469 (mm-40) REVERT: P 22 GLN cc_start: 0.8063 (pt0) cc_final: 0.7800 (pt0) REVERT: Q 29 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9001 (mm) REVERT: R 28 TRP cc_start: 0.7181 (t-100) cc_final: 0.6731 (t60) REVERT: R 45 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7114 (ttt180) REVERT: R 49 ARG cc_start: 0.7140 (ttm170) cc_final: 0.6807 (ttt-90) REVERT: S 90 GLU cc_start: 0.8448 (tt0) cc_final: 0.7430 (tm-30) REVERT: T 29 ARG cc_start: 0.8113 (ttt180) cc_final: 0.7769 (tpp-160) outliers start: 33 outliers final: 14 residues processed: 448 average time/residue: 0.2588 time to fit residues: 163.5179 Evaluate side-chains 407 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 392 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 76 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12324 Z= 0.226 Angle : 0.658 13.909 16689 Z= 0.325 Chirality : 0.043 0.220 1971 Planarity : 0.004 0.061 2066 Dihedral : 4.096 17.574 1686 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.03 % Allowed : 18.20 % Favored : 78.77 % 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: 0.94 (0.21), residues: 1558 helix: 1.29 (0.15), residues: 1101 sheet: -0.84 (0.54), residues: 87 loop : -0.91 (0.33), residues: 370 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 0.017 0.001 TYR 3 49 ARG 0.006 0.001 ARG P 39 *********************** 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 457 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 419 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8492 (t) cc_final: 0.8082 (m) REVERT: 6 49 TYR cc_start: 0.7706 (m-10) cc_final: 0.7472 (m-80) REVERT: 6 60 MET cc_start: 0.6899 (mmm) cc_final: 0.6649 (mmt) REVERT: 8 66 MET cc_start: 0.7658 (ttp) cc_final: 0.6784 (mmt) REVERT: 2 39 ASN cc_start: 0.8240 (t0) cc_final: 0.7795 (t0) REVERT: 3 1 ASP cc_start: 0.7045 (p0) cc_final: 0.6527 (t70) REVERT: G 104 MET cc_start: 0.7667 (mmt) cc_final: 0.7177 (mmm) REVERT: H 25 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7210 (tm-30) REVERT: H 136 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8350 (mt-10) REVERT: H 139 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8442 (mt-10) REVERT: I 14 ARG cc_start: 0.8088 (tpt90) cc_final: 0.7433 (ttm-80) REVERT: I 18 ILE cc_start: 0.9029 (mt) cc_final: 0.8619 (mp) REVERT: K 26 TYR cc_start: 0.7504 (t80) cc_final: 0.6773 (t80) REVERT: M 159 ASN cc_start: 0.8074 (p0) cc_final: 0.7798 (p0) REVERT: N 55 LYS cc_start: 0.9025 (mtpp) cc_final: 0.8530 (mtmt) REVERT: N 115 MET cc_start: 0.8847 (ppp) cc_final: 0.8527 (ppp) REVERT: N 118 ARG cc_start: 0.6895 (mtp180) cc_final: 0.5688 (mmt-90) REVERT: N 145 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7657 (mm-30) REVERT: P 13 MET cc_start: 0.8373 (mmm) cc_final: 0.7693 (mmm) REVERT: R 28 TRP cc_start: 0.7195 (t-100) cc_final: 0.6612 (t60) REVERT: R 45 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7111 (ttt180) REVERT: R 49 ARG cc_start: 0.7149 (ttm170) cc_final: 0.6817 (ttt-90) REVERT: S 70 LYS cc_start: 0.7587 (tppt) cc_final: 0.6716 (mttm) REVERT: S 71 GLU cc_start: 0.8500 (mp0) cc_final: 0.8013 (pm20) REVERT: S 73 VAL cc_start: 0.9131 (t) cc_final: 0.8931 (p) REVERT: T 21 LEU cc_start: 0.8678 (mt) cc_final: 0.8110 (tt) REVERT: T 29 ARG cc_start: 0.7997 (ttt180) cc_final: 0.7785 (tpp-160) outliers start: 38 outliers final: 21 residues processed: 437 average time/residue: 0.2541 time to fit residues: 159.1935 Evaluate side-chains 406 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 385 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 58 GLU Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 51 ILE Chi-restraints excluded: chain 1 residue 70 LEU Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 3 residue 57 SER Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 0.0060 chunk 92 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 45 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 22 GLN R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12324 Z= 0.200 Angle : 0.665 10.269 16689 Z= 0.323 Chirality : 0.042 0.172 1971 Planarity : 0.004 0.045 2066 Dihedral : 4.096 17.773 1686 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.95 % Allowed : 21.47 % 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: 1.34 (0.22), residues: 1558 helix: 1.42 (0.16), residues: 1127 sheet: -0.56 (0.55), residues: 87 loop : -0.30 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 25 HIS 0.003 0.001 HIS R 83 PHE 0.031 0.002 PHE S 64 TYR 0.015 0.001 TYR 4 49 ARG 0.007 0.001 ARG S 47 *********************** 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 439 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 402 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.8006 (mttm) cc_final: 0.7695 (mttm) REVERT: 4 48 SER cc_start: 0.8491 (t) cc_final: 0.8056 (m) REVERT: 6 49 TYR cc_start: 0.7630 (m-10) cc_final: 0.7410 (m-80) REVERT: 6 60 MET cc_start: 0.6817 (mmm) cc_final: 0.6567 (mmt) REVERT: 7 45 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7652 (tm-30) REVERT: 8 66 MET cc_start: 0.7664 (ttp) cc_final: 0.6776 (mmt) REVERT: 2 39 ASN cc_start: 0.8214 (t0) cc_final: 0.7795 (t0) REVERT: 3 1 ASP cc_start: 0.6994 (p0) cc_final: 0.6556 (t70) REVERT: G 104 MET cc_start: 0.7635 (mmt) cc_final: 0.7139 (mmm) REVERT: H 109 LYS cc_start: 0.8856 (tptp) cc_final: 0.8621 (mtpt) REVERT: H 136 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8403 (mt-10) REVERT: H 139 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8347 (mt-10) REVERT: I 14 ARG cc_start: 0.8078 (tpt90) cc_final: 0.7430 (ttm-80) REVERT: I 18 ILE cc_start: 0.9026 (mt) cc_final: 0.8644 (mp) REVERT: K 26 TYR cc_start: 0.7549 (t80) cc_final: 0.6935 (t80) REVERT: M 159 ASN cc_start: 0.8108 (p0) cc_final: 0.7898 (p0) REVERT: N 55 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8585 (mtpt) REVERT: N 115 MET cc_start: 0.8872 (ppp) cc_final: 0.8505 (ppp) REVERT: N 118 ARG cc_start: 0.6898 (mtp180) cc_final: 0.5735 (mmt-90) REVERT: N 140 MET cc_start: 0.8237 (pmm) cc_final: 0.7834 (pmm) REVERT: N 145 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7626 (mm-30) REVERT: P 13 MET cc_start: 0.8418 (mmm) cc_final: 0.7861 (mmm) REVERT: R 28 TRP cc_start: 0.7124 (t-100) cc_final: 0.6553 (t60) REVERT: R 45 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7128 (ttt180) REVERT: R 49 ARG cc_start: 0.7177 (ttm170) cc_final: 0.6851 (ttt-90) REVERT: R 62 ILE cc_start: 0.8344 (tp) cc_final: 0.8028 (mt) REVERT: S 71 GLU cc_start: 0.8416 (mp0) cc_final: 0.8079 (pm20) REVERT: S 73 VAL cc_start: 0.9154 (t) cc_final: 0.8931 (p) REVERT: S 90 GLU cc_start: 0.8419 (tt0) cc_final: 0.7434 (tm-30) REVERT: T 5 VAL cc_start: 0.8654 (t) cc_final: 0.8451 (t) REVERT: T 21 LEU cc_start: 0.8688 (mt) cc_final: 0.8114 (tt) outliers start: 37 outliers final: 21 residues processed: 416 average time/residue: 0.2506 time to fit residues: 146.8341 Evaluate side-chains 400 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 379 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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 5 residue 28 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 7 residue 62 LEU Chi-restraints excluded: chain 8 residue 65 LEU Chi-restraints excluded: chain 1 residue 18 VAL 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 H residue 125 GLU 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 Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain T residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN 8 44 GLN ** N 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12324 Z= 0.197 Angle : 0.651 9.482 16689 Z= 0.320 Chirality : 0.042 0.247 1971 Planarity : 0.004 0.045 2066 Dihedral : 4.086 16.867 1686 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.51 % Allowed : 22.35 % Favored : 74.14 % 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: 1.57 (0.16), residues: 1126 sheet: -0.66 (0.62), residues: 70 loop : -0.29 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 25 HIS 0.004 0.001 HIS R 83 PHE 0.021 0.002 PHE 7 63 TYR 0.018 0.001 TYR K 44 ARG 0.010 0.000 ARG S 47 *********************** 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 440 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 396 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.8001 (mttm) cc_final: 0.7747 (mttm) REVERT: 4 48 SER cc_start: 0.8510 (t) cc_final: 0.8067 (m) REVERT: 6 32 LEU cc_start: 0.8301 (tt) cc_final: 0.8089 (tt) REVERT: 6 49 TYR cc_start: 0.7591 (m-10) cc_final: 0.7330 (m-80) REVERT: 6 60 MET cc_start: 0.6757 (mmm) cc_final: 0.6450 (mmt) REVERT: 7 45 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7744 (tm-30) REVERT: 7 58 GLU cc_start: 0.8043 (tp30) cc_final: 0.7711 (tp30) REVERT: 8 45 GLN cc_start: 0.6577 (tp40) cc_final: 0.6287 (tp40) REVERT: 8 66 MET cc_start: 0.7717 (ttp) cc_final: 0.6799 (mmt) REVERT: 2 39 ASN cc_start: 0.8229 (t0) cc_final: 0.7822 (t0) REVERT: 3 1 ASP cc_start: 0.6992 (p0) cc_final: 0.6567 (t70) REVERT: G 104 MET cc_start: 0.7716 (mmt) cc_final: 0.7198 (mmm) REVERT: H 136 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8359 (mt-10) REVERT: H 139 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8389 (mt-10) REVERT: I 13 ILE cc_start: 0.8947 (mm) cc_final: 0.8601 (mm) REVERT: I 14 ARG cc_start: 0.8072 (tpt90) cc_final: 0.7697 (ttm-80) REVERT: I 18 ILE cc_start: 0.9005 (mt) cc_final: 0.8757 (mm) REVERT: K 26 TYR cc_start: 0.7580 (t80) cc_final: 0.6933 (t80) REVERT: N 55 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8604 (mtpt) REVERT: N 115 MET cc_start: 0.8854 (ppp) cc_final: 0.8469 (ppp) REVERT: N 118 ARG cc_start: 0.6927 (mtp180) cc_final: 0.5681 (mmt-90) REVERT: N 145 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7632 (mm-30) REVERT: P 13 MET cc_start: 0.8400 (mmm) cc_final: 0.7860 (mmm) REVERT: R 30 LEU cc_start: 0.7880 (pp) cc_final: 0.7408 (mp) REVERT: R 45 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7146 (ttt180) REVERT: R 49 ARG cc_start: 0.7172 (ttm170) cc_final: 0.6832 (ttt-90) REVERT: R 62 ILE cc_start: 0.8380 (tp) cc_final: 0.8075 (mt) REVERT: S 54 LYS cc_start: 0.9408 (mmmt) cc_final: 0.9112 (tptp) REVERT: S 70 LYS cc_start: 0.7949 (tppt) cc_final: 0.7125 (mttm) REVERT: S 71 GLU cc_start: 0.8362 (mp0) cc_final: 0.8126 (mp0) REVERT: S 87 TYR cc_start: 0.8016 (m-80) cc_final: 0.7642 (m-10) REVERT: S 90 GLU cc_start: 0.8462 (tt0) cc_final: 0.7469 (tm-30) REVERT: T 21 LEU cc_start: 0.8672 (mt) cc_final: 0.8127 (tt) outliers start: 44 outliers final: 29 residues processed: 418 average time/residue: 0.2596 time to fit residues: 154.9887 Evaluate side-chains 408 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 379 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 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 3 residue 57 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 43 LEU 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 R residue 65 ILE Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 0.4980 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** P 22 GLN R 83 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4385 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= 0.204 Angle : 0.662 10.707 16689 Z= 0.326 Chirality : 0.042 0.246 1971 Planarity : 0.004 0.045 2066 Dihedral : 4.066 17.557 1686 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.91 % Allowed : 23.38 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.64 (0.22), residues: 1558 helix: 1.66 (0.16), residues: 1123 sheet: -0.52 (0.64), residues: 70 loop : -0.25 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.025 0.002 PHE 3 69 TYR 0.026 0.001 TYR 3 49 ARG 0.008 0.000 ARG S 47 *********************** 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 453 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 404 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8496 (t) cc_final: 0.8061 (m) REVERT: 6 49 TYR cc_start: 0.7588 (m-10) cc_final: 0.7318 (m-80) REVERT: 6 60 MET cc_start: 0.6690 (mmm) cc_final: 0.6436 (mmt) REVERT: 8 66 MET cc_start: 0.7765 (ttp) cc_final: 0.6814 (mmt) REVERT: 2 39 ASN cc_start: 0.8198 (t0) cc_final: 0.7771 (t0) REVERT: 2 47 PHE cc_start: 0.8181 (t80) cc_final: 0.7706 (t80) REVERT: 3 1 ASP cc_start: 0.6927 (p0) cc_final: 0.6574 (t70) REVERT: 3 60 MET cc_start: 0.7175 (mtm) cc_final: 0.6790 (mtp) REVERT: G 36 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7759 (ttp80) REVERT: G 104 MET cc_start: 0.7711 (mmt) cc_final: 0.7205 (mmm) REVERT: H 135 ILE cc_start: 0.8803 (mm) cc_final: 0.7688 (mm) REVERT: H 136 GLU cc_start: 0.8721 (mt-10) cc_final: 0.7997 (mt-10) REVERT: H 139 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8003 (mp0) REVERT: I 14 ARG cc_start: 0.8107 (tpt90) cc_final: 0.7703 (tpm170) REVERT: K 7 GLU cc_start: 0.7279 (tt0) cc_final: 0.6912 (tp30) REVERT: K 26 TYR cc_start: 0.7584 (t80) cc_final: 0.6861 (t80) REVERT: K 84 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8024 (ttpt) REVERT: K 85 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8963 (tt) REVERT: K 88 GLN cc_start: 0.8412 (mp10) cc_final: 0.8107 (mp10) REVERT: M 141 GLU cc_start: 0.8590 (pt0) cc_final: 0.8194 (pm20) REVERT: N 22 LEU cc_start: 0.8594 (mp) cc_final: 0.8324 (tt) REVERT: N 55 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8611 (mtpt) REVERT: N 115 MET cc_start: 0.8870 (ppp) cc_final: 0.8490 (ppp) REVERT: N 118 ARG cc_start: 0.6946 (mtp180) cc_final: 0.5707 (mmt-90) REVERT: N 140 MET cc_start: 0.8248 (pmm) cc_final: 0.7840 (pmm) REVERT: N 145 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7650 (mm-30) REVERT: P 13 MET cc_start: 0.8355 (mmm) cc_final: 0.7738 (mmm) REVERT: R 30 LEU cc_start: 0.7980 (pp) cc_final: 0.7573 (mp) REVERT: R 45 ARG cc_start: 0.7949 (mtm180) cc_final: 0.7140 (ttt180) REVERT: R 49 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6923 (ttt-90) REVERT: R 62 ILE cc_start: 0.8383 (tp) cc_final: 0.8025 (mt) REVERT: S 50 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8854 (pm20) REVERT: S 54 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9093 (tptp) REVERT: S 70 LYS cc_start: 0.8002 (tppt) cc_final: 0.7417 (mttt) REVERT: S 71 GLU cc_start: 0.8346 (mp0) cc_final: 0.8100 (mp0) REVERT: S 87 TYR cc_start: 0.7986 (m-80) cc_final: 0.7737 (m-10) REVERT: T 21 LEU cc_start: 0.8624 (mt) cc_final: 0.8104 (tt) outliers start: 49 outliers final: 33 residues processed: 431 average time/residue: 0.2550 time to fit residues: 156.3466 Evaluate side-chains 423 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 388 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 28 VAL Chi-restraints excluded: chain 5 residue 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER Chi-restraints excluded: chain 8 residue 51 ILE 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 96 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 THR 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 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 S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 50 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN 3 45 GLN N 152 GLN ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12324 Z= 0.205 Angle : 0.670 11.003 16689 Z= 0.332 Chirality : 0.042 0.244 1971 Planarity : 0.004 0.051 2066 Dihedral : 4.068 20.220 1686 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.91 % Allowed : 25.78 % Favored : 70.31 % 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: 1.66 (0.22), residues: 1558 helix: 1.61 (0.15), residues: 1134 sheet: -0.29 (0.58), residues: 86 loop : -0.11 (0.36), residues: 338 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 0.034 0.002 PHE 8 54 TYR 0.023 0.002 TYR T 32 ARG 0.009 0.000 ARG S 47 *********************** 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 451 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 402 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 7 LYS cc_start: 0.7977 (mttm) cc_final: 0.7769 (mttm) REVERT: 4 48 SER cc_start: 0.8498 (t) cc_final: 0.8048 (m) REVERT: 6 32 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8044 (tt) REVERT: 6 49 TYR cc_start: 0.7545 (m-10) cc_final: 0.7293 (m-80) REVERT: 6 60 MET cc_start: 0.6687 (mmm) cc_final: 0.6427 (mmt) REVERT: 8 66 MET cc_start: 0.7763 (ttp) cc_final: 0.6810 (mmt) REVERT: 2 39 ASN cc_start: 0.8153 (t0) cc_final: 0.7756 (t0) REVERT: 3 1 ASP cc_start: 0.6859 (p0) cc_final: 0.6613 (t70) REVERT: 3 54 PHE cc_start: 0.8413 (t80) cc_final: 0.8208 (t80) REVERT: 3 60 MET cc_start: 0.7152 (mtm) cc_final: 0.6783 (mtp) REVERT: G 36 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7748 (ttp80) REVERT: G 104 MET cc_start: 0.7714 (mmt) cc_final: 0.7195 (mmm) REVERT: H 109 LYS cc_start: 0.8885 (tptp) cc_final: 0.8444 (mmmt) REVERT: H 130 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7748 (tp30) REVERT: H 135 ILE cc_start: 0.8810 (mm) cc_final: 0.7657 (mm) REVERT: H 136 GLU cc_start: 0.8715 (mt-10) cc_final: 0.7952 (mt-10) REVERT: H 139 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8009 (mp0) REVERT: I 14 ARG cc_start: 0.8091 (tpt90) cc_final: 0.7791 (ttm-80) REVERT: I 18 ILE cc_start: 0.8988 (mt) cc_final: 0.8558 (mm) REVERT: K 7 GLU cc_start: 0.7320 (tt0) cc_final: 0.6941 (tp30) REVERT: K 26 TYR cc_start: 0.7644 (t80) cc_final: 0.6967 (t80) REVERT: K 84 LYS cc_start: 0.8880 (ttmt) cc_final: 0.7947 (ttpt) REVERT: K 85 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8887 (tt) REVERT: K 88 GLN cc_start: 0.8342 (mp10) cc_final: 0.7904 (mp10) REVERT: M 141 GLU cc_start: 0.8600 (pt0) cc_final: 0.8200 (pm20) REVERT: N 22 LEU cc_start: 0.8605 (mp) cc_final: 0.8316 (tt) REVERT: N 55 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8601 (mtpt) REVERT: N 118 ARG cc_start: 0.7155 (mtp180) cc_final: 0.5718 (mmt-90) REVERT: N 140 MET cc_start: 0.8189 (pmm) cc_final: 0.7823 (pmm) REVERT: N 145 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7652 (mm-30) REVERT: P 23 GLU cc_start: 0.8770 (mp0) cc_final: 0.8521 (mp0) REVERT: R 30 LEU cc_start: 0.7963 (pp) cc_final: 0.7561 (mp) REVERT: R 45 ARG cc_start: 0.7940 (mtm180) cc_final: 0.7141 (ttt180) REVERT: R 49 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6903 (ttt-90) REVERT: R 62 ILE cc_start: 0.8396 (tp) cc_final: 0.8043 (mt) REVERT: S 54 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9117 (tptp) REVERT: S 77 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8083 (pp) REVERT: S 87 TYR cc_start: 0.7987 (m-80) cc_final: 0.7702 (m-10) REVERT: T 21 LEU cc_start: 0.8601 (mt) cc_final: 0.8109 (tt) REVERT: T 33 LEU cc_start: 0.9371 (mp) cc_final: 0.9163 (mp) REVERT: T 34 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8678 (mmmm) outliers start: 49 outliers final: 35 residues processed: 424 average time/residue: 0.2516 time to fit residues: 150.4546 Evaluate side-chains 426 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 388 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 51 ILE 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 54 PHE Chi-restraints excluded: chain 5 residue 58 GLU Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER 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 28 VAL Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 75 MET Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 175 GLU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 THR 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 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 THR 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 90 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 2 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 ** S 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12324 Z= 0.233 Angle : 0.706 13.183 16689 Z= 0.351 Chirality : 0.044 0.349 1971 Planarity : 0.004 0.052 2066 Dihedral : 4.087 16.999 1686 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.59 % Allowed : 25.86 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.22), residues: 1558 helix: 1.63 (0.15), residues: 1127 sheet: -0.21 (0.59), residues: 86 loop : -0.15 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 28 HIS 0.003 0.001 HIS R 83 PHE 0.036 0.002 PHE 8 54 TYR 0.030 0.002 TYR N 221 ARG 0.011 0.000 ARG S 47 *********************** 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 436 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 391 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8476 (t) cc_final: 0.8019 (m) REVERT: 6 32 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.8013 (tt) REVERT: 6 60 MET cc_start: 0.6706 (mmm) cc_final: 0.6432 (mmt) REVERT: 8 66 MET cc_start: 0.7790 (ttp) cc_final: 0.6825 (mmt) REVERT: 2 39 ASN cc_start: 0.8213 (t0) cc_final: 0.7816 (t0) REVERT: G 36 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7713 (ttp80) REVERT: G 104 MET cc_start: 0.7750 (mmt) cc_final: 0.7266 (mmm) REVERT: H 32 ASN cc_start: 0.8418 (m-40) cc_final: 0.8002 (t0) REVERT: H 128 ARG cc_start: 0.7853 (mmt90) cc_final: 0.7615 (mtp85) REVERT: H 135 ILE cc_start: 0.8850 (mm) cc_final: 0.7685 (mm) REVERT: H 136 GLU cc_start: 0.8752 (mt-10) cc_final: 0.7923 (mt-10) REVERT: H 139 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8006 (mp0) REVERT: I 14 ARG cc_start: 0.8079 (tpt90) cc_final: 0.7773 (ttm-80) REVERT: I 18 ILE cc_start: 0.8993 (mt) cc_final: 0.8687 (mm) REVERT: K 7 GLU cc_start: 0.7324 (tt0) cc_final: 0.6969 (tp30) REVERT: K 26 TYR cc_start: 0.7610 (t80) cc_final: 0.6911 (t80) REVERT: K 84 LYS cc_start: 0.8904 (ttmt) cc_final: 0.7873 (ttpt) REVERT: K 85 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8845 (tt) REVERT: K 88 GLN cc_start: 0.8336 (mp10) cc_final: 0.7902 (mp10) REVERT: M 141 GLU cc_start: 0.8626 (pt0) cc_final: 0.8228 (pm20) REVERT: N 22 LEU cc_start: 0.8627 (mp) cc_final: 0.8316 (tt) REVERT: N 55 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8608 (mtpt) REVERT: N 118 ARG cc_start: 0.7235 (mtp180) cc_final: 0.5617 (mmt-90) REVERT: N 140 MET cc_start: 0.8278 (pmm) cc_final: 0.7836 (pmm) REVERT: N 145 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7642 (mm-30) REVERT: P 13 MET cc_start: 0.8454 (mmm) cc_final: 0.8069 (mmm) REVERT: P 39 ARG cc_start: 0.8802 (mtp-110) cc_final: 0.8305 (mtp180) REVERT: R 30 LEU cc_start: 0.7952 (pp) cc_final: 0.7544 (mp) REVERT: R 45 ARG cc_start: 0.7941 (mtm180) cc_final: 0.7144 (ttt180) REVERT: R 49 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6928 (ttt-90) REVERT: R 62 ILE cc_start: 0.8412 (tp) cc_final: 0.8064 (mt) REVERT: S 54 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9162 (tptp) REVERT: S 77 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8112 (pp) REVERT: S 87 TYR cc_start: 0.7987 (m-80) cc_final: 0.7713 (m-10) REVERT: T 21 LEU cc_start: 0.8608 (mt) cc_final: 0.8133 (tt) REVERT: T 34 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8713 (mmmm) outliers start: 45 outliers final: 34 residues processed: 410 average time/residue: 0.2452 time to fit residues: 142.3922 Evaluate side-chains 414 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 377 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 32 LEU Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER 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 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 G residue 96 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 THR 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 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 6 THR Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain S residue 77 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 4.9990 chunk 127 optimal weight: 0.0470 chunk 135 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 45 GLN 3 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 ** S 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12324 Z= 0.203 Angle : 0.704 12.940 16689 Z= 0.347 Chirality : 0.044 0.344 1971 Planarity : 0.004 0.052 2066 Dihedral : 4.093 17.842 1686 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.35 % Allowed : 26.50 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1558 helix: 1.65 (0.15), residues: 1146 sheet: -0.15 (0.59), residues: 86 loop : 0.02 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.035 0.002 PHE 8 54 TYR 0.018 0.001 TYR K 44 ARG 0.010 0.001 ARG T 42 *********************** 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 437 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 395 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8465 (t) cc_final: 0.7999 (m) REVERT: 6 32 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7974 (tt) REVERT: 6 49 TYR cc_start: 0.7548 (m-80) cc_final: 0.7024 (m-80) REVERT: 6 60 MET cc_start: 0.6674 (mmm) cc_final: 0.6282 (mmt) REVERT: 8 66 MET cc_start: 0.7750 (ttp) cc_final: 0.6730 (mmt) REVERT: 2 39 ASN cc_start: 0.8147 (t0) cc_final: 0.7782 (t0) REVERT: 2 47 PHE cc_start: 0.8148 (t80) cc_final: 0.7642 (t80) REVERT: G 104 MET cc_start: 0.7733 (mmt) cc_final: 0.7237 (mmm) REVERT: G 140 ASP cc_start: 0.6737 (m-30) cc_final: 0.5578 (m-30) REVERT: H 32 ASN cc_start: 0.8417 (m-40) cc_final: 0.7988 (t0) REVERT: H 128 ARG cc_start: 0.7829 (mmt90) cc_final: 0.7603 (mtp85) REVERT: H 135 ILE cc_start: 0.8841 (mm) cc_final: 0.7697 (mm) REVERT: H 136 GLU cc_start: 0.8737 (mt-10) cc_final: 0.7950 (mt-10) REVERT: H 139 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8021 (mp0) REVERT: I 14 ARG cc_start: 0.8030 (tpt90) cc_final: 0.7619 (ttm-80) REVERT: K 14 TYR cc_start: 0.7989 (m-80) cc_final: 0.7727 (m-80) REVERT: K 26 TYR cc_start: 0.7604 (t80) cc_final: 0.6900 (t80) REVERT: K 84 LYS cc_start: 0.8921 (ttmt) cc_final: 0.7844 (ttpt) REVERT: K 85 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8840 (tt) REVERT: K 88 GLN cc_start: 0.8312 (mp10) cc_final: 0.7887 (mp10) REVERT: M 141 GLU cc_start: 0.8628 (pt0) cc_final: 0.7980 (pm20) REVERT: N 22 LEU cc_start: 0.8623 (mp) cc_final: 0.8306 (tt) REVERT: N 55 LYS cc_start: 0.9001 (mtpp) cc_final: 0.8579 (mtpt) REVERT: N 115 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8434 (ppp) REVERT: N 118 ARG cc_start: 0.7168 (mtp180) cc_final: 0.5654 (mmt-90) REVERT: N 140 MET cc_start: 0.8301 (pmm) cc_final: 0.7809 (pmm) REVERT: N 145 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7642 (mm-30) REVERT: N 152 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8129 (mp10) REVERT: P 13 MET cc_start: 0.8423 (mmm) cc_final: 0.8030 (mmm) REVERT: P 39 ARG cc_start: 0.8812 (mtp-110) cc_final: 0.8396 (mtp180) REVERT: R 30 LEU cc_start: 0.7919 (pp) cc_final: 0.7513 (mp) REVERT: R 45 ARG cc_start: 0.7938 (mtm180) cc_final: 0.7152 (ttt180) REVERT: R 49 ARG cc_start: 0.7189 (ttm170) cc_final: 0.6912 (ttt-90) REVERT: S 47 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7893 (tmm160) REVERT: S 54 LYS cc_start: 0.9429 (mmmt) cc_final: 0.9167 (tptp) REVERT: S 77 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8156 (pp) REVERT: T 21 LEU cc_start: 0.8621 (mt) cc_final: 0.8178 (tt) REVERT: T 33 LEU cc_start: 0.9380 (mp) cc_final: 0.9160 (mp) REVERT: T 34 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8778 (mmmm) outliers start: 42 outliers final: 34 residues processed: 413 average time/residue: 0.2537 time to fit residues: 146.9802 Evaluate side-chains 419 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 381 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 3 ASP Chi-restraints excluded: chain 4 residue 28 VAL Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 5 residue 28 VAL Chi-restraints excluded: chain 5 residue 69 PHE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER 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 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 G residue 96 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 THR 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 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 100 MET Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR 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 87 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 127 optimal weight: 0.0270 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12324 Z= 0.223 Angle : 0.724 13.613 16689 Z= 0.355 Chirality : 0.044 0.355 1971 Planarity : 0.004 0.078 2066 Dihedral : 4.158 17.522 1686 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.51 % Allowed : 26.82 % Favored : 69.67 % 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: 1.71 (0.22), residues: 1558 helix: 1.65 (0.15), residues: 1130 sheet: -0.07 (0.58), residues: 85 loop : -0.12 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.004 0.001 HIS R 83 PHE 0.042 0.002 PHE 4 54 TYR 0.018 0.001 TYR K 44 ARG 0.008 0.001 ARG S 47 ********************** 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 434 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 390 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 48 SER cc_start: 0.8485 (t) cc_final: 0.8024 (m) REVERT: 6 32 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7961 (tt) REVERT: 6 45 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5914 (tp40) REVERT: 6 49 TYR cc_start: 0.7630 (m-80) cc_final: 0.7190 (m-80) REVERT: 6 60 MET cc_start: 0.6602 (mmm) cc_final: 0.6357 (mmt) REVERT: 8 66 MET cc_start: 0.7750 (ttp) cc_final: 0.6719 (mmt) REVERT: 2 39 ASN cc_start: 0.8184 (t0) cc_final: 0.7800 (t0) REVERT: G 104 MET cc_start: 0.7783 (mmt) cc_final: 0.7322 (mmm) REVERT: H 32 ASN cc_start: 0.8422 (m-40) cc_final: 0.8016 (t0) REVERT: H 128 ARG cc_start: 0.7844 (mmt90) cc_final: 0.7608 (mtp85) REVERT: H 135 ILE cc_start: 0.8867 (mm) cc_final: 0.7723 (mm) REVERT: H 139 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8006 (mp0) REVERT: K 13 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7981 (ptm160) REVERT: K 14 TYR cc_start: 0.7994 (m-80) cc_final: 0.7763 (m-80) REVERT: K 26 TYR cc_start: 0.7592 (t80) cc_final: 0.6873 (t80) REVERT: K 84 LYS cc_start: 0.8939 (ttmt) cc_final: 0.7845 (ttpt) REVERT: K 85 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8829 (tt) REVERT: K 88 GLN cc_start: 0.8308 (mp10) cc_final: 0.7872 (mp10) REVERT: M 141 GLU cc_start: 0.8630 (pt0) cc_final: 0.7970 (pm20) REVERT: N 22 LEU cc_start: 0.8636 (mp) cc_final: 0.8295 (tt) REVERT: N 55 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8579 (mtpt) REVERT: N 115 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8576 (ppp) REVERT: N 118 ARG cc_start: 0.7206 (mtp180) cc_final: 0.5710 (mmt-90) REVERT: N 140 MET cc_start: 0.8322 (pmm) cc_final: 0.7795 (pmm) REVERT: N 145 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7650 (mm-30) REVERT: N 152 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8164 (mp10) REVERT: N 181 MET cc_start: 0.8405 (mmp) cc_final: 0.8056 (tpp) REVERT: P 13 MET cc_start: 0.8472 (mmm) cc_final: 0.8077 (mmm) REVERT: P 39 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8423 (mtp180) REVERT: Q 12 MET cc_start: 0.9348 (tpp) cc_final: 0.9103 (mmt) REVERT: R 30 LEU cc_start: 0.7923 (pp) cc_final: 0.7521 (mp) REVERT: R 45 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7166 (ttt180) REVERT: R 49 ARG cc_start: 0.7204 (ttm170) cc_final: 0.6918 (ttt-90) REVERT: R 62 ILE cc_start: 0.8411 (tp) cc_final: 0.8051 (mt) REVERT: S 54 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9213 (tptp) REVERT: S 70 LYS cc_start: 0.7924 (tppt) cc_final: 0.7055 (mmtt) REVERT: S 77 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8166 (pp) REVERT: T 21 LEU cc_start: 0.8639 (mt) cc_final: 0.8198 (tt) REVERT: T 34 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8788 (mmmm) outliers start: 44 outliers final: 36 residues processed: 409 average time/residue: 0.2517 time to fit residues: 145.9086 Evaluate side-chains 421 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 380 time to evaluate : 1.916 ------------------------------------------------------------------------------- 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 69 PHE Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 6 residue 32 LEU Chi-restraints excluded: chain 6 residue 45 GLN Chi-restraints excluded: chain 6 residue 51 ILE Chi-restraints excluded: chain 6 residue 71 ILE Chi-restraints excluded: chain 7 residue 31 SER 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 28 VAL Chi-restraints excluded: chain 2 residue 72 LEU Chi-restraints excluded: chain 3 residue 57 SER Chi-restraints excluded: chain 3 residue 64 CYS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 THR Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 SER Chi-restraints excluded: chain K residue 61 LEU Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 36 GLU Chi-restraints excluded: chain S residue 41 THR 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 36 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 105 optimal weight: 0.0670 chunk 6 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.145603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116791 restraints weight = 22963.763| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.66 r_work: 0.3494 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.343 12324 Z= 0.411 Angle : 0.944 65.894 16689 Z= 0.528 Chirality : 0.045 0.451 1971 Planarity : 0.008 0.299 2066 Dihedral : 4.154 17.456 1686 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.35 % Allowed : 26.74 % Favored : 69.91 % Cbeta Deviations : 0.07 % 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: 1.72 (0.22), residues: 1558 helix: 1.65 (0.15), residues: 1130 sheet: -0.06 (0.58), residues: 85 loop : -0.12 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.004 0.001 HIS N 127 PHE 0.034 0.002 PHE 4 54 TYR 0.017 0.001 TYR K 44 ARG 0.024 0.001 ARG K 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3760.06 seconds wall clock time: 69 minutes 17.40 seconds (4157.40 seconds total)