Starting phenix.real_space_refine on Sat Aug 23 14:45:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9f_34565/08_2025/8h9f_34565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9f_34565/08_2025/8h9f_34565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h9f_34565/08_2025/8h9f_34565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9f_34565/08_2025/8h9f_34565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9f_34565/08_2025/8h9f_34565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9f_34565/08_2025/8h9f_34565.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 63 5.16 5 C 8059 2.51 5 N 1938 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12265 Number of models: 1 Model: "" Number of chains: 22 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: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "3" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 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: "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 Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Time building chain proxies: 3.28, per 1000 atoms: 0.27 Number of scatterers: 12265 At special positions: 0 Unit cell: (112.42, 104.39, 137.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 5 15.00 O 2200 8.00 N 1938 7.00 C 8059 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: 1.16 Conformation dependent library (CDL) restraints added in 670.1 milliseconds Enol-peptide restraints added in 1.7 microseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 5 sheets defined 77.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain '1' and resid 2 through 15 Processing helix chain '1' and resid 17 through 39 removed outlier: 4.276A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 removed outlier: 3.516A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 removed outlier: 3.610A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 2 61 " --> pdb=" O SER 2 57 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 17 removed outlier: 4.040A 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: 3.517A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 3 61 " --> pdb=" O SER 3 57 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 removed outlier: 3.850A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL 4 67 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 16 Processing helix chain '5' and resid 17 through 39 removed outlier: 4.427A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 73 removed outlier: 3.679A pdb=" N GLU 5 58 " --> pdb=" O PHE 5 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 4.045A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 39 removed outlier: 4.428A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 16 Processing helix chain '7' and resid 17 through 39 removed outlier: 4.404A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.553A pdb=" N PHE 7 73 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.984A 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: 3.550A pdb=" N ALA 8 59 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE 8 73 " --> pdb=" O PHE 8 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 49 removed outlier: 3.979A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.655A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 109 through 118 removed outlier: 3.690A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.552A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 187 through 193 removed outlier: 3.540A pdb=" N SER G 191 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.687A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.296A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.560A 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: 4.615A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 97 removed outlier: 3.891A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.524A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'N' and resid 6 through 10 removed outlier: 3.645A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.641A 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 85 removed outlier: 3.670A pdb=" N THR N 81 " --> pdb=" O ILE N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.881A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.003A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 138 removed outlier: 3.513A pdb=" N LEU N 137 " --> pdb=" O PRO N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 181 removed outlier: 3.559A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) Proline residue: N 153 - end of helix Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'P' and resid 4 through 9 Processing helix chain 'P' and resid 9 through 19 removed outlier: 3.598A pdb=" N MET P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Proline residue: P 15 - end of helix removed outlier: 3.552A 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 7 removed outlier: 5.605A pdb=" N THR Q 6 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR Q 7 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 22 removed outlier: 3.533A pdb=" N MET Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 removed outlier: 3.657A pdb=" N ASN Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.749A 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 79 removed outlier: 4.387A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.694A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU S 36 " --> pdb=" O TYR S 32 " (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 93 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 3.861A 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: 5.113A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA G 127 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 5.216A pdb=" N ASN H 29 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N PHE H 20 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY H 80 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.286A 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 Processing sheet with id=AA5, first strand: chain 'N' and resid 13 through 14 949 hydrogen bonds defined for protein. 2788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1910 1.31 - 1.43: 3225 1.43 - 1.56: 7244 1.56 - 1.68: 11 1.68 - 1.81: 115 Bond restraints: 12505 Sorted by residual: bond pdb=" C ARG 2 38 " pdb=" O ARG 2 38 " ideal model delta sigma weight residual 1.236 1.296 -0.060 1.19e-02 7.06e+03 2.51e+01 bond pdb=" C ARG 3 38 " pdb=" CA AARG 3 38 " ideal model delta sigma weight residual 1.522 1.583 -0.061 1.37e-02 5.33e+03 1.98e+01 bond pdb=" C ARG 2 38 " pdb=" CA AARG 2 38 " ideal model delta sigma weight residual 1.524 1.580 -0.056 1.32e-02 5.74e+03 1.82e+01 bond pdb=" C31 3PH Q 101 " pdb=" O31 3PH Q 101 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C21 3PH Q 101 " pdb=" O21 3PH Q 101 " ideal model delta sigma weight residual 1.328 1.400 -0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 12500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 16407 1.78 - 3.56: 396 3.56 - 5.33: 84 5.33 - 7.11: 17 7.11 - 8.89: 3 Bond angle restraints: 16907 Sorted by residual: angle pdb=" O ARG 2 38 " pdb=" C ARG 2 38 " pdb=" CA BARG 2 38 " ideal model delta sigma weight residual 120.42 126.91 -6.49 1.06e+00 8.90e-01 3.75e+01 angle pdb=" O ARG 2 38 " pdb=" C ARG 2 38 " pdb=" CA AARG 2 38 " ideal model delta sigma weight residual 120.24 126.98 -6.74 1.11e+00 8.12e-01 3.68e+01 angle pdb=" C LEU N 137 " pdb=" N ILE N 138 " pdb=" CA ILE N 138 " ideal model delta sigma weight residual 120.24 123.89 -3.65 6.30e-01 2.52e+00 3.36e+01 angle pdb=" N ARG 2 38 " pdb=" CA BARG 2 38 " pdb=" C ARG 2 38 " ideal model delta sigma weight residual 111.36 117.11 -5.75 1.09e+00 8.42e-01 2.78e+01 angle pdb=" N SER G 121 " pdb=" CA SER G 121 " pdb=" C SER G 121 " ideal model delta sigma weight residual 113.43 106.80 6.63 1.26e+00 6.30e-01 2.77e+01 ... (remaining 16902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 7086 27.06 - 54.12: 288 54.12 - 81.18: 40 81.18 - 108.24: 2 108.24 - 135.30: 1 Dihedral angle restraints: 7417 sinusoidal: 2871 harmonic: 4546 Sorted by residual: dihedral pdb=" CD BARG 2 38 " pdb=" NE BARG 2 38 " pdb=" CZ BARG 2 38 " pdb=" NH1BARG 2 38 " ideal model delta sinusoidal sigma weight residual 0.00 -61.88 61.88 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CA LEU H 145 " pdb=" C LEU H 145 " pdb=" N GLU H 146 " pdb=" CA GLU H 146 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA5 CDL R 101 " pdb=" CA4 CDL R 101 " pdb=" OA6 CDL R 101 " pdb=" CA6 CDL R 101 " ideal model delta sinusoidal sigma weight residual 168.24 -56.46 -135.30 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 7414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1407 0.042 - 0.085: 428 0.085 - 0.127: 121 0.127 - 0.169: 16 0.169 - 0.212: 6 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CA ILE 4 71 " pdb=" N ILE 4 71 " pdb=" C ILE 4 71 " pdb=" CB ILE 4 71 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE P 5 " pdb=" N ILE P 5 " pdb=" C ILE P 5 " pdb=" CB ILE P 5 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA VAL H 77 " pdb=" N VAL H 77 " pdb=" C VAL H 77 " pdb=" CB VAL H 77 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1975 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG 2 38 " 0.962 9.50e-02 1.11e+02 4.31e-01 1.12e+02 pdb=" NE BARG 2 38 " -0.058 2.00e-02 2.50e+03 pdb=" CZ BARG 2 38 " -0.009 2.00e-02 2.50e+03 pdb=" NH1BARG 2 38 " 0.002 2.00e-02 2.50e+03 pdb=" NH2BARG 2 38 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 14 " 0.429 9.50e-02 1.11e+02 1.92e-01 2.26e+01 pdb=" NE ARG I 14 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG I 14 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG I 14 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 14 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 3 38 " 0.036 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" O ARG 3 38 " -0.014 2.00e-02 2.50e+03 pdb=" CA AARG 3 38 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN 3 39 " -0.012 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1151 2.74 - 3.28: 13035 3.28 - 3.82: 20859 3.82 - 4.36: 25655 4.36 - 4.90: 43674 Nonbonded interactions: 104374 Sorted by model distance: nonbonded pdb=" O ARG N 66 " pdb=" OG SER N 69 " model vdw 2.198 3.040 nonbonded pdb=" O LYS G 63 " pdb=" NZ LYS G 101 " model vdw 2.235 3.120 nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.263 3.120 nonbonded pdb=" NZ LYS Q 27 " pdb=" O32 3PH Q 101 " model vdw 2.302 3.120 nonbonded pdb=" O GLY G 114 " pdb=" NH1 ARG G 118 " model vdw 2.308 3.120 ... (remaining 104369 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' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '2' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '3' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '4' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '5' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '6' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '7' and (resid 1 through 37 or resid 39 through 75)) selection = (chain '8' and (resid 1 through 37 or resid 39 through 75)) } 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=0.50 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: 11.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.540 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:8.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 0.072 12505 Z= 0.269 Angle : 0.689 8.890 16907 Z= 0.404 Chirality : 0.045 0.212 1978 Planarity : 0.011 0.431 2080 Dihedral : 14.638 135.299 4517 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.16 % Allowed : 2.87 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.19), residues: 1560 helix: -1.16 (0.14), residues: 1115 sheet: -0.87 (0.54), residues: 88 loop : -2.48 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 13 TYR 0.015 0.001 TYR I 12 PHE 0.019 0.002 PHE 8 29 TRP 0.013 0.001 TRP P 10 HIS 0.004 0.001 HIS G 120 Details of bonding type rmsd covalent geometry : bond 0.00520 (12505) covalent geometry : angle 0.68859 (16907) hydrogen bonds : bond 0.14327 ( 943) hydrogen bonds : angle 6.99351 ( 2788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.420 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7614 (m-80) cc_final: 0.6829 (t80) REVERT: 5 75 MET cc_start: 0.4321 (mtp) cc_final: 0.3877 (mtt) REVERT: 6 7 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7635 (mttp) REVERT: 8 60 MET cc_start: 0.7882 (mmm) cc_final: 0.7360 (mmp) REVERT: G 64 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7394 (mmmt) REVERT: G 75 ARG cc_start: 0.7588 (mtp85) cc_final: 0.6779 (ptt180) REVERT: Q 28 MET cc_start: 0.8342 (mmp) cc_final: 0.7775 (mmp) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.5948 time to fit residues: 151.5993 Evaluate side-chains 205 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 44 GLN G 120 HIS G 163 ASN H 15 GLN H 85 ASN H 111 ASN K 88 GLN M 136 ASN N 46 GLN N 47 GLN N 61 HIS N 123 ASN N 172 HIS ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN S 75 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108799 restraints weight = 28166.706| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.85 r_work: 0.3082 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12505 Z= 0.156 Angle : 0.564 6.838 16907 Z= 0.302 Chirality : 0.041 0.189 1978 Planarity : 0.004 0.058 2080 Dihedral : 10.821 137.781 1842 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.31 % Allowed : 10.28 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1560 helix: 0.68 (0.15), residues: 1108 sheet: -0.66 (0.55), residues: 90 loop : -1.71 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 13 TYR 0.012 0.001 TYR I 12 PHE 0.020 0.002 PHE R 79 TRP 0.016 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00320 (12505) covalent geometry : angle 0.56411 (16907) hydrogen bonds : bond 0.05898 ( 943) hydrogen bonds : angle 4.78947 ( 2788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.358 Fit side-chains REVERT: 2 75 MET cc_start: 0.4402 (tpt) cc_final: 0.4160 (ttm) REVERT: 4 69 PHE cc_start: 0.6926 (m-80) cc_final: 0.5592 (t80) REVERT: 5 75 MET cc_start: 0.4112 (mtp) cc_final: 0.3547 (mtt) REVERT: 6 7 LYS cc_start: 0.7115 (mtmt) cc_final: 0.6562 (mttp) REVERT: 8 60 MET cc_start: 0.7284 (mmm) cc_final: 0.7051 (mmp) REVERT: G 75 ARG cc_start: 0.7372 (mtp85) cc_final: 0.5795 (ptt180) REVERT: G 130 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7943 (mt-10) REVERT: G 147 GLU cc_start: 0.7623 (mp0) cc_final: 0.7314 (mm-30) REVERT: H 32 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7397 (m-40) REVERT: I 7 GLN cc_start: 0.7270 (mm110) cc_final: 0.6994 (mt0) REVERT: N 56 GLN cc_start: 0.8266 (tp40) cc_final: 0.7958 (mm-40) REVERT: N 181 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6556 (ttm) REVERT: N 199 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7937 (tt) REVERT: Q 28 MET cc_start: 0.8688 (mmp) cc_final: 0.8367 (mmp) outliers start: 28 outliers final: 7 residues processed: 227 average time/residue: 0.6007 time to fit residues: 147.3484 Evaluate side-chains 220 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 12 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 139 optimal weight: 0.0030 chunk 125 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104086 restraints weight = 23739.573| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.30 r_work: 0.3111 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12505 Z= 0.169 Angle : 0.554 8.131 16907 Z= 0.294 Chirality : 0.042 0.198 1978 Planarity : 0.004 0.039 2080 Dihedral : 10.376 139.105 1842 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.79 % Allowed : 13.31 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.21), residues: 1560 helix: 1.40 (0.15), residues: 1110 sheet: -0.59 (0.54), residues: 91 loop : -1.23 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 118 TYR 0.012 0.001 TYR I 12 PHE 0.022 0.001 PHE R 79 TRP 0.014 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00376 (12505) covalent geometry : angle 0.55444 (16907) hydrogen bonds : bond 0.05656 ( 943) hydrogen bonds : angle 4.51054 ( 2788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.463 Fit side-chains REVERT: 4 69 PHE cc_start: 0.6856 (m-80) cc_final: 0.5531 (t80) REVERT: 5 75 MET cc_start: 0.4102 (mtp) cc_final: 0.3519 (mtt) REVERT: 6 7 LYS cc_start: 0.7072 (mtmt) cc_final: 0.6545 (mttp) REVERT: G 35 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: G 64 LYS cc_start: 0.7508 (mmtp) cc_final: 0.6622 (mmmt) REVERT: G 75 ARG cc_start: 0.7425 (mtp85) cc_final: 0.5816 (ptt180) REVERT: G 130 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7996 (mt-10) REVERT: G 147 GLU cc_start: 0.7675 (mp0) cc_final: 0.7248 (mm-30) REVERT: G 154 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6982 (mm-30) REVERT: G 195 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: N 56 GLN cc_start: 0.8274 (tp40) cc_final: 0.7969 (mm-40) REVERT: Q 28 MET cc_start: 0.8713 (mmp) cc_final: 0.8425 (mmp) outliers start: 34 outliers final: 9 residues processed: 227 average time/residue: 0.5455 time to fit residues: 134.5146 Evaluate side-chains 219 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109802 restraints weight = 18859.699| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.99 r_work: 0.3157 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12505 Z= 0.137 Angle : 0.521 7.976 16907 Z= 0.276 Chirality : 0.040 0.194 1978 Planarity : 0.004 0.038 2080 Dihedral : 10.121 140.637 1842 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.71 % Allowed : 14.42 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.21), residues: 1560 helix: 1.77 (0.15), residues: 1109 sheet: -0.45 (0.54), residues: 91 loop : -0.94 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 13 TYR 0.010 0.001 TYR G 44 PHE 0.027 0.001 PHE R 79 TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00281 (12505) covalent geometry : angle 0.52099 (16907) hydrogen bonds : bond 0.05162 ( 943) hydrogen bonds : angle 4.34728 ( 2788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.484 Fit side-chains REVERT: 1 60 MET cc_start: 0.7035 (mmt) cc_final: 0.6829 (mmt) REVERT: 4 69 PHE cc_start: 0.6865 (m-80) cc_final: 0.5614 (t80) REVERT: 5 38 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7881 (mtt-85) REVERT: 5 75 MET cc_start: 0.4176 (mtp) cc_final: 0.3656 (mtt) REVERT: G 35 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: G 64 LYS cc_start: 0.7431 (mmtp) cc_final: 0.6512 (mmmt) REVERT: G 75 ARG cc_start: 0.7390 (mtp85) cc_final: 0.5785 (ptt180) REVERT: G 147 GLU cc_start: 0.7615 (mp0) cc_final: 0.7248 (mm-30) REVERT: G 195 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: H 146 GLU cc_start: 0.5336 (OUTLIER) cc_final: 0.5114 (mt-10) REVERT: K 7 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8079 (tp30) REVERT: N 56 GLN cc_start: 0.8300 (tp40) cc_final: 0.8014 (mm-40) REVERT: N 181 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6285 (tpp) REVERT: N 199 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7884 (tt) REVERT: S 84 MET cc_start: 0.7274 (mmp) cc_final: 0.7071 (mmp) outliers start: 33 outliers final: 10 residues processed: 221 average time/residue: 0.6130 time to fit residues: 147.1014 Evaluate side-chains 219 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 4 residue 62 LEU Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 5 ASN R 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102871 restraints weight = 22166.308| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.31 r_work: 0.3076 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12505 Z= 0.192 Angle : 0.566 8.278 16907 Z= 0.298 Chirality : 0.043 0.194 1978 Planarity : 0.004 0.038 2080 Dihedral : 10.078 140.121 1842 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.11 % Allowed : 15.86 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1560 helix: 1.82 (0.15), residues: 1104 sheet: -0.37 (0.54), residues: 89 loop : -0.81 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 41 TYR 0.015 0.001 TYR I 12 PHE 0.024 0.002 PHE R 79 TRP 0.011 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00447 (12505) covalent geometry : angle 0.56556 (16907) hydrogen bonds : bond 0.05761 ( 943) hydrogen bonds : angle 4.39587 ( 2788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 0.506 Fit side-chains REVERT: 4 69 PHE cc_start: 0.6828 (m-80) cc_final: 0.5582 (t80) REVERT: 5 75 MET cc_start: 0.4158 (mtp) cc_final: 0.3617 (mtt) REVERT: 6 7 LYS cc_start: 0.7060 (mtmt) cc_final: 0.6510 (mttp) REVERT: G 35 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: G 75 ARG cc_start: 0.7354 (mtp85) cc_final: 0.5685 (ptt180) REVERT: G 147 GLU cc_start: 0.7610 (mp0) cc_final: 0.7220 (mm-30) REVERT: G 154 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: G 195 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8058 (m-30) REVERT: H 146 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.5268 (mt-10) REVERT: K 7 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: K 14 TYR cc_start: 0.8798 (m-80) cc_final: 0.8556 (m-80) REVERT: N 181 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6456 (tpp) REVERT: N 199 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7755 (tt) REVERT: Q 28 MET cc_start: 0.8673 (mmp) cc_final: 0.8391 (mmp) REVERT: R 44 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7162 (mt0) REVERT: S 84 MET cc_start: 0.7280 (mmp) cc_final: 0.7060 (mmp) REVERT: S 94 LYS cc_start: 0.7047 (pttp) cc_final: 0.6707 (pttp) REVERT: T 32 TYR cc_start: 0.6726 (m-10) cc_final: 0.6486 (m-10) outliers start: 38 outliers final: 12 residues processed: 223 average time/residue: 0.5717 time to fit residues: 138.5764 Evaluate side-chains 225 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain R residue 44 GLN Chi-restraints excluded: chain S residue 85 TRP Chi-restraints excluded: chain S residue 92 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 67 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 GLN Q 5 ASN R 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107927 restraints weight = 20637.908| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.13 r_work: 0.3132 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12505 Z= 0.143 Angle : 0.527 8.673 16907 Z= 0.278 Chirality : 0.041 0.168 1978 Planarity : 0.004 0.038 2080 Dihedral : 9.954 141.041 1842 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.95 % Allowed : 15.70 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.21), residues: 1560 helix: 2.00 (0.15), residues: 1104 sheet: -0.26 (0.54), residues: 89 loop : -0.67 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 133 TYR 0.011 0.001 TYR I 12 PHE 0.025 0.001 PHE R 79 TRP 0.010 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00304 (12505) covalent geometry : angle 0.52748 (16907) hydrogen bonds : bond 0.05255 ( 943) hydrogen bonds : angle 4.29405 ( 2788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.457 Fit side-chains REVERT: 1 66 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5733 (tmm) REVERT: 4 69 PHE cc_start: 0.6905 (m-80) cc_final: 0.5643 (t80) REVERT: 5 38 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7992 (mtt-85) REVERT: 5 75 MET cc_start: 0.4203 (mtp) cc_final: 0.3661 (mtt) REVERT: 7 75 MET cc_start: 0.7549 (mtm) cc_final: 0.7211 (pmm) REVERT: G 75 ARG cc_start: 0.7428 (mtp85) cc_final: 0.5814 (ptt180) REVERT: G 147 GLU cc_start: 0.7630 (mp0) cc_final: 0.7187 (mm-30) REVERT: G 154 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: G 195 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: H 32 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7704 (m-40) REVERT: H 146 GLU cc_start: 0.5397 (OUTLIER) cc_final: 0.5165 (mt-10) REVERT: K 7 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8172 (tp30) REVERT: N 181 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6545 (tpp) REVERT: N 199 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7887 (tt) REVERT: R 44 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: S 85 TRP cc_start: 0.8085 (OUTLIER) cc_final: 0.6400 (m-90) REVERT: S 94 LYS cc_start: 0.7149 (pttp) cc_final: 0.6891 (pttp) REVERT: T 32 TYR cc_start: 0.6716 (m-10) cc_final: 0.6508 (m-10) outliers start: 36 outliers final: 11 residues processed: 224 average time/residue: 0.5598 time to fit residues: 136.3706 Evaluate side-chains 217 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 44 GLN Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105517 restraints weight = 20727.356| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.18 r_work: 0.3127 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12505 Z= 0.154 Angle : 0.540 9.327 16907 Z= 0.283 Chirality : 0.041 0.180 1978 Planarity : 0.004 0.037 2080 Dihedral : 9.891 142.096 1842 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.71 % Allowed : 16.49 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.21), residues: 1560 helix: 2.04 (0.15), residues: 1104 sheet: -0.24 (0.53), residues: 89 loop : -0.61 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 128 TYR 0.015 0.001 TYR G 193 PHE 0.025 0.001 PHE R 79 TRP 0.009 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00340 (12505) covalent geometry : angle 0.54034 (16907) hydrogen bonds : bond 0.05299 ( 943) hydrogen bonds : angle 4.27382 ( 2788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.466 Fit side-chains REVERT: 1 66 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5655 (tmm) REVERT: 4 69 PHE cc_start: 0.6818 (m-80) cc_final: 0.5584 (t80) REVERT: 5 38 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7945 (mtt-85) REVERT: 5 75 MET cc_start: 0.4136 (mtp) cc_final: 0.3577 (mtt) REVERT: 7 75 MET cc_start: 0.7586 (mtm) cc_final: 0.7266 (pmm) REVERT: G 75 ARG cc_start: 0.7398 (mtp85) cc_final: 0.5774 (ptt180) REVERT: G 147 GLU cc_start: 0.7578 (mp0) cc_final: 0.7212 (mm-30) REVERT: G 154 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: G 195 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: H 146 GLU cc_start: 0.5379 (OUTLIER) cc_final: 0.5143 (mt-10) REVERT: I 37 LYS cc_start: 0.8617 (ttmt) cc_final: 0.7903 (tmtt) REVERT: K 7 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: N 147 ILE cc_start: 0.7976 (mt) cc_final: 0.7713 (pt) REVERT: N 181 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6541 (tpp) REVERT: N 199 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7845 (tt) REVERT: R 44 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.7234 (mt0) REVERT: S 85 TRP cc_start: 0.8010 (OUTLIER) cc_final: 0.6305 (m-90) REVERT: T 32 TYR cc_start: 0.6677 (m-10) cc_final: 0.6472 (m-10) outliers start: 33 outliers final: 11 residues processed: 213 average time/residue: 0.5591 time to fit residues: 129.2709 Evaluate side-chains 216 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 44 GLN Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 145 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 137 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 56 optimal weight: 0.0010 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106359 restraints weight = 28386.385| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.57 r_work: 0.3141 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12505 Z= 0.126 Angle : 0.520 10.350 16907 Z= 0.271 Chirality : 0.040 0.185 1978 Planarity : 0.003 0.039 2080 Dihedral : 9.680 143.800 1842 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.23 % Allowed : 17.21 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.21), residues: 1560 helix: 2.19 (0.15), residues: 1103 sheet: -0.32 (0.53), residues: 89 loop : -0.48 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 45 TYR 0.012 0.001 TYR G 193 PHE 0.025 0.001 PHE R 79 TRP 0.009 0.001 TRP P 10 HIS 0.002 0.000 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00251 (12505) covalent geometry : angle 0.51963 (16907) hydrogen bonds : bond 0.04892 ( 943) hydrogen bonds : angle 4.18235 ( 2788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.416 Fit side-chains REVERT: 3 25 ILE cc_start: 0.8649 (mt) cc_final: 0.8371 (mp) REVERT: 4 69 PHE cc_start: 0.6748 (m-80) cc_final: 0.5500 (t80) REVERT: 5 38 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7912 (mtt-85) REVERT: 5 75 MET cc_start: 0.4142 (mtp) cc_final: 0.3566 (mtt) REVERT: 7 75 MET cc_start: 0.7547 (mtm) cc_final: 0.7324 (pmm) REVERT: G 75 ARG cc_start: 0.7401 (mtp85) cc_final: 0.5791 (ptt180) REVERT: G 147 GLU cc_start: 0.7537 (mp0) cc_final: 0.7100 (mm-30) REVERT: G 195 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: K 7 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: N 56 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7889 (mm-40) REVERT: N 147 ILE cc_start: 0.7931 (mt) cc_final: 0.7662 (pt) REVERT: N 181 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6518 (tpp) REVERT: N 199 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7792 (tt) REVERT: R 69 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7419 (mp) REVERT: S 85 TRP cc_start: 0.8021 (OUTLIER) cc_final: 0.6298 (m-90) REVERT: T 32 TYR cc_start: 0.6711 (m-10) cc_final: 0.6497 (m-10) outliers start: 27 outliers final: 11 residues processed: 223 average time/residue: 0.5077 time to fit residues: 123.5260 Evaluate side-chains 217 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 chunk 28 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105515 restraints weight = 28423.042| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.64 r_work: 0.3131 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12505 Z= 0.135 Angle : 0.534 10.636 16907 Z= 0.277 Chirality : 0.041 0.185 1978 Planarity : 0.003 0.039 2080 Dihedral : 9.564 145.297 1842 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.99 % Allowed : 17.93 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.21), residues: 1560 helix: 2.22 (0.15), residues: 1103 sheet: -0.29 (0.53), residues: 89 loop : -0.45 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 13 TYR 0.012 0.001 TYR G 193 PHE 0.025 0.001 PHE R 79 TRP 0.007 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00284 (12505) covalent geometry : angle 0.53377 (16907) hydrogen bonds : bond 0.04974 ( 943) hydrogen bonds : angle 4.17515 ( 2788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.455 Fit side-chains REVERT: 3 25 ILE cc_start: 0.8586 (mt) cc_final: 0.8313 (mp) REVERT: 4 69 PHE cc_start: 0.6675 (m-80) cc_final: 0.5425 (t80) REVERT: 5 38 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7840 (mtt-85) REVERT: 5 75 MET cc_start: 0.4071 (mtp) cc_final: 0.3540 (mtt) REVERT: G 75 ARG cc_start: 0.7304 (mtp85) cc_final: 0.5744 (ptt180) REVERT: G 147 GLU cc_start: 0.7393 (mp0) cc_final: 0.6996 (mm-30) REVERT: G 154 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6984 (mm-30) REVERT: G 195 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: K 7 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8107 (tp30) REVERT: N 56 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7839 (mm-40) REVERT: N 147 ILE cc_start: 0.7960 (mt) cc_final: 0.7666 (pt) REVERT: N 181 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6553 (tpp) REVERT: N 199 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7792 (tt) REVERT: S 85 TRP cc_start: 0.7932 (OUTLIER) cc_final: 0.6160 (m-90) REVERT: T 32 TYR cc_start: 0.6639 (m-10) cc_final: 0.6432 (m-10) outliers start: 24 outliers final: 11 residues processed: 220 average time/residue: 0.5879 time to fit residues: 141.0825 Evaluate side-chains 214 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 88 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 ASN N 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106072 restraints weight = 22018.579| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.26 r_work: 0.3141 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12505 Z= 0.147 Angle : 0.545 11.733 16907 Z= 0.283 Chirality : 0.041 0.188 1978 Planarity : 0.004 0.039 2080 Dihedral : 9.515 145.877 1842 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.75 % Allowed : 18.33 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.21), residues: 1560 helix: 2.22 (0.15), residues: 1103 sheet: -0.15 (0.53), residues: 89 loop : -0.44 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 13 TYR 0.014 0.001 TYR G 193 PHE 0.025 0.001 PHE R 79 TRP 0.008 0.001 TRP P 10 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00323 (12505) covalent geometry : angle 0.54515 (16907) hydrogen bonds : bond 0.05105 ( 943) hydrogen bonds : angle 4.20937 ( 2788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.511 Fit side-chains REVERT: 1 66 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5624 (tmm) REVERT: 3 25 ILE cc_start: 0.8688 (mt) cc_final: 0.8437 (mp) REVERT: 4 69 PHE cc_start: 0.6712 (m-80) cc_final: 0.5415 (t80) REVERT: 5 38 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7934 (mtt-85) REVERT: 5 75 MET cc_start: 0.4070 (mtp) cc_final: 0.3538 (mtt) REVERT: G 75 ARG cc_start: 0.7372 (mtp85) cc_final: 0.5781 (ptt180) REVERT: G 147 GLU cc_start: 0.7539 (mp0) cc_final: 0.7157 (mm-30) REVERT: G 154 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: G 195 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: K 7 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: N 56 GLN cc_start: 0.8289 (tp-100) cc_final: 0.7949 (mm-40) REVERT: N 147 ILE cc_start: 0.7986 (mt) cc_final: 0.7662 (pt) REVERT: N 181 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6570 (tpp) REVERT: N 199 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7903 (tt) REVERT: S 85 TRP cc_start: 0.8028 (OUTLIER) cc_final: 0.6226 (m-90) REVERT: T 32 TYR cc_start: 0.6706 (m-10) cc_final: 0.6496 (m-10) outliers start: 21 outliers final: 10 residues processed: 210 average time/residue: 0.5852 time to fit residues: 133.9393 Evaluate side-chains 215 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 84 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 66 optimal weight: 0.0570 chunk 101 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 ASN P 8 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106476 restraints weight = 24637.430| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.40 r_work: 0.3145 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12505 Z= 0.137 Angle : 0.541 11.820 16907 Z= 0.280 Chirality : 0.041 0.184 1978 Planarity : 0.003 0.039 2080 Dihedral : 9.411 146.428 1842 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.67 % Allowed : 18.25 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.21), residues: 1560 helix: 2.26 (0.15), residues: 1103 sheet: -0.26 (0.53), residues: 89 loop : -0.39 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 13 TYR 0.013 0.001 TYR G 193 PHE 0.025 0.001 PHE R 79 TRP 0.008 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00293 (12505) covalent geometry : angle 0.54095 (16907) hydrogen bonds : bond 0.04958 ( 943) hydrogen bonds : angle 4.17967 ( 2788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5993.75 seconds wall clock time: 102 minutes 40.44 seconds (6160.44 seconds total)