Starting phenix.real_space_refine on Wed Jul 30 21:19:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9f_34565/07_2025/8h9f_34565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9f_34565/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2025/8h9f_34565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2025/8h9f_34565.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2025/8h9f_34565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2025/8h9f_34565.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 10.38, per 1000 atoms: 0.85 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: 3.40 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.00 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: 3.73 Time building geometry restraints manager: 3.95 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: 54.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.490 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.720 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP P 10 HIS 0.004 0.001 HIS G 120 PHE 0.019 0.002 PHE 8 29 TYR 0.015 0.001 TYR I 12 ARG 0.003 0.000 ARG K 13 Details of bonding type rmsd hydrogen bonds : bond 0.14327 ( 943) hydrogen bonds : angle 6.99351 ( 2788) covalent geometry : bond 0.00520 (12505) covalent geometry : angle 0.68859 (16907) *********************** 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 : 1.252 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: 1.3587 time to fit residues: 346.7698 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 : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.0270 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 137 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.145441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108822 restraints weight = 16547.618| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.98 r_work: 0.3155 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12505 Z= 0.149 Angle : 0.558 6.427 16907 Z= 0.299 Chirality : 0.041 0.183 1978 Planarity : 0.004 0.058 2080 Dihedral : 10.746 138.196 1842 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.31 % Allowed : 10.36 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1560 helix: 0.75 (0.15), residues: 1109 sheet: -0.64 (0.55), residues: 90 loop : -1.64 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.022 0.001 PHE R 79 TYR 0.010 0.001 TYR I 12 ARG 0.005 0.000 ARG K 13 Details of bonding type rmsd hydrogen bonds : bond 0.05722 ( 943) hydrogen bonds : angle 4.71898 ( 2788) covalent geometry : bond 0.00296 (12505) covalent geometry : angle 0.55842 (16907) *********************** 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 248 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 2.665 Fit side-chains REVERT: 2 75 MET cc_start: 0.4457 (tpt) cc_final: 0.4212 (ttm) REVERT: 4 69 PHE cc_start: 0.6927 (m-80) cc_final: 0.5587 (t80) REVERT: 5 75 MET cc_start: 0.4053 (mtp) cc_final: 0.3498 (mtt) REVERT: 6 7 LYS cc_start: 0.7139 (mtmt) cc_final: 0.6589 (mttp) REVERT: 8 60 MET cc_start: 0.7252 (mmm) cc_final: 0.7002 (mmp) REVERT: G 64 LYS cc_start: 0.7448 (mmtt) cc_final: 0.6665 (mmmt) REVERT: G 75 ARG cc_start: 0.7391 (mtp85) cc_final: 0.5716 (ptt90) REVERT: G 130 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7949 (mt-10) REVERT: G 147 GLU cc_start: 0.7675 (mp0) cc_final: 0.7372 (mm-30) REVERT: H 32 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7410 (m-40) REVERT: N 56 GLN cc_start: 0.8296 (tp40) cc_final: 0.7995 (mm-40) REVERT: N 199 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7964 (tt) REVERT: Q 28 MET cc_start: 0.8730 (mmp) cc_final: 0.8440 (mmp) REVERT: R 91 LYS cc_start: 0.7399 (tmmt) cc_final: 0.7162 (tmmt) outliers start: 28 outliers final: 6 residues processed: 228 average time/residue: 1.6973 time to fit residues: 419.2146 Evaluate side-chains 212 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 H residue 32 ASN Chi-restraints excluded: chain I residue 29 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 82 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 14 optimal weight: 5.9990 chunk 99 optimal weight: 0.0980 chunk 149 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3693 r_free = 0.3693 target = 0.143424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104298 restraints weight = 24895.966| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.35 r_work: 0.3109 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12505 Z= 0.161 Angle : 0.548 8.225 16907 Z= 0.290 Chirality : 0.041 0.203 1978 Planarity : 0.004 0.039 2080 Dihedral : 10.373 139.854 1842 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.39 % Allowed : 14.02 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1560 helix: 1.44 (0.15), residues: 1109 sheet: -0.58 (0.54), residues: 91 loop : -1.19 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 PHE 0.025 0.001 PHE R 79 TYR 0.012 0.001 TYR I 12 ARG 0.003 0.000 ARG K 13 Details of bonding type rmsd hydrogen bonds : bond 0.05606 ( 943) hydrogen bonds : angle 4.47867 ( 2788) covalent geometry : bond 0.00353 (12505) covalent geometry : angle 0.54755 (16907) *********************** 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 243 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.262 Fit side-chains REVERT: 4 69 PHE cc_start: 0.6924 (m-80) cc_final: 0.5601 (t80) REVERT: 5 38 ARG cc_start: 0.8237 (mtt180) cc_final: 0.7918 (mtt-85) REVERT: 5 75 MET cc_start: 0.4140 (mtp) cc_final: 0.3577 (mtt) REVERT: 6 7 LYS cc_start: 0.7140 (mtmt) cc_final: 0.6603 (mttp) REVERT: G 35 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: G 64 LYS cc_start: 0.7476 (mmtt) cc_final: 0.6696 (mmmt) REVERT: G 75 ARG cc_start: 0.7359 (mtp85) cc_final: 0.5736 (ptt180) REVERT: G 147 GLU cc_start: 0.7699 (mp0) cc_final: 0.7329 (mm-30) REVERT: G 154 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: G 195 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: K 83 ASP cc_start: 0.8142 (m-30) cc_final: 0.7932 (m-30) REVERT: N 56 GLN cc_start: 0.8308 (tp40) cc_final: 0.8003 (mm-40) REVERT: N 181 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6435 (tpp) REVERT: Q 28 MET cc_start: 0.8750 (mmp) cc_final: 0.8469 (mmp) outliers start: 29 outliers final: 6 residues processed: 225 average time/residue: 1.2996 time to fit residues: 317.8909 Evaluate side-chains 217 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 181 MET 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 73 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 139 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109236 restraints weight = 18615.154| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.01 r_work: 0.3159 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1832 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 : 0.514 7.904 16907 Z= 0.272 Chirality : 0.040 0.194 1978 Planarity : 0.004 0.037 2080 Dihedral : 10.106 141.419 1842 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.55 % Allowed : 14.66 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1560 helix: 1.86 (0.15), residues: 1103 sheet: -0.44 (0.54), residues: 91 loop : -0.83 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.024 0.001 PHE R 79 TYR 0.010 0.001 TYR G 44 ARG 0.003 0.000 ARG G 133 Details of bonding type rmsd hydrogen bonds : bond 0.05127 ( 943) hydrogen bonds : angle 4.31008 ( 2788) covalent geometry : bond 0.00278 (12505) covalent geometry : angle 0.51359 (16907) *********************** 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 237 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 1.316 Fit side-chains REVERT: 4 69 PHE cc_start: 0.6821 (m-80) cc_final: 0.5559 (t80) REVERT: 5 38 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7839 (mtt-85) REVERT: 5 75 MET cc_start: 0.4082 (mtp) cc_final: 0.3579 (mtt) REVERT: G 35 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: G 75 ARG cc_start: 0.7350 (mtp85) cc_final: 0.5748 (ptt180) REVERT: G 147 GLU cc_start: 0.7585 (mp0) cc_final: 0.7194 (mm-30) REVERT: G 195 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: K 7 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: K 83 ASP cc_start: 0.8029 (m-30) cc_final: 0.7822 (m-30) REVERT: N 56 GLN cc_start: 0.8246 (tp40) cc_final: 0.7956 (mm-40) REVERT: N 181 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6259 (tpp) REVERT: N 199 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7836 (tt) REVERT: S 84 MET cc_start: 0.7218 (mmp) cc_final: 0.7013 (mmp) REVERT: S 94 LYS cc_start: 0.6984 (pttp) cc_final: 0.6654 (pttp) outliers start: 31 outliers final: 10 residues processed: 217 average time/residue: 1.2327 time to fit residues: 290.5359 Evaluate side-chains 219 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 71 ILE 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 110 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 118 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 42 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3719 r_free = 0.3719 target = 0.145956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105814 restraints weight = 23577.441| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.40 r_work: 0.3134 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 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 = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1939 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= 0.142 Angle : 0.520 8.147 16907 Z= 0.274 Chirality : 0.041 0.191 1978 Planarity : 0.004 0.038 2080 Dihedral : 9.937 142.484 1842 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.03 % Allowed : 15.54 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.21), residues: 1560 helix: 2.00 (0.15), residues: 1103 sheet: -0.40 (0.53), residues: 91 loop : -0.64 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.024 0.001 PHE R 79 TYR 0.013 0.001 TYR G 193 ARG 0.002 0.000 ARG K 13 Details of bonding type rmsd hydrogen bonds : bond 0.05156 ( 943) hydrogen bonds : angle 4.25060 ( 2788) covalent geometry : bond 0.00304 (12505) covalent geometry : angle 0.51955 (16907) *********************** 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 247 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 1.659 Fit side-chains REVERT: 1 66 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5571 (tmm) REVERT: 4 69 PHE cc_start: 0.6835 (m-80) cc_final: 0.5581 (t80) REVERT: 5 38 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7906 (mtt-85) REVERT: 5 75 MET cc_start: 0.4097 (mtp) cc_final: 0.3594 (mtt) REVERT: 7 75 MET cc_start: 0.7548 (mtm) cc_final: 0.7137 (pmm) REVERT: G 35 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: G 75 ARG cc_start: 0.7382 (mtp85) cc_final: 0.5773 (ptt180) REVERT: G 147 GLU cc_start: 0.7595 (mp0) cc_final: 0.7219 (mm-30) REVERT: G 154 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: G 195 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: K 7 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: K 83 ASP cc_start: 0.8065 (m-30) cc_final: 0.7837 (m-30) REVERT: N 143 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7308 (mp) REVERT: N 181 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6395 (tpp) REVERT: N 199 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7894 (tt) REVERT: S 94 LYS cc_start: 0.6938 (pttp) cc_final: 0.6603 (pttp) REVERT: T 32 TYR cc_start: 0.6666 (m-10) cc_final: 0.6431 (m-10) outliers start: 37 outliers final: 9 residues processed: 226 average time/residue: 1.2517 time to fit residues: 309.2795 Evaluate side-chains 223 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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 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 143 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 132 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 127 optimal weight: 0.2980 chunk 139 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 56 GLN R 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105851 restraints weight = 23650.474| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.40 r_work: 0.3141 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 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 = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2067 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 : 0.516 8.740 16907 Z= 0.271 Chirality : 0.040 0.161 1978 Planarity : 0.003 0.038 2080 Dihedral : 9.787 143.425 1842 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.71 % Allowed : 16.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.21), residues: 1560 helix: 2.12 (0.15), residues: 1103 sheet: -0.32 (0.53), residues: 91 loop : -0.55 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 PHE 0.024 0.001 PHE R 79 TYR 0.012 0.001 TYR G 193 ARG 0.003 0.000 ARG G 133 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 943) hydrogen bonds : angle 4.20620 ( 2788) covalent geometry : bond 0.00289 (12505) covalent geometry : angle 0.51563 (16907) *********************** 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 244 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 1.478 Fit side-chains REVERT: 1 66 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5572 (tmm) REVERT: 3 25 ILE cc_start: 0.8679 (mt) cc_final: 0.8411 (mp) REVERT: 4 69 PHE cc_start: 0.6782 (m-80) cc_final: 0.5545 (t80) REVERT: 5 38 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7926 (mtt-85) REVERT: 5 75 MET cc_start: 0.4014 (mtp) cc_final: 0.3510 (mtt) REVERT: 7 75 MET cc_start: 0.7606 (mtm) cc_final: 0.7171 (pmm) REVERT: G 35 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: G 75 ARG cc_start: 0.7389 (mtp85) cc_final: 0.5718 (ptt90) REVERT: G 130 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8018 (mm-30) REVERT: G 147 GLU cc_start: 0.7592 (mp0) cc_final: 0.7162 (mm-30) REVERT: G 195 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: K 7 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8167 (tp30) REVERT: N 56 GLN cc_start: 0.8288 (tp40) cc_final: 0.8024 (mm-40) REVERT: N 181 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6375 (tpp) REVERT: N 199 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7892 (tt) REVERT: S 85 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.6317 (m-90) REVERT: T 32 TYR cc_start: 0.6707 (m-10) cc_final: 0.6495 (m-10) outliers start: 33 outliers final: 8 residues processed: 225 average time/residue: 1.4697 time to fit residues: 359.2981 Evaluate side-chains 217 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 35 GLU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 195 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.145839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107023 restraints weight = 22312.246| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.27 r_work: 0.3154 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 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 = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2163 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= 0.134 Angle : 0.518 9.714 16907 Z= 0.271 Chirality : 0.041 0.194 1978 Planarity : 0.003 0.039 2080 Dihedral : 9.574 145.015 1842 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.63 % Allowed : 16.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.21), residues: 1560 helix: 2.19 (0.15), residues: 1102 sheet: -0.14 (0.53), residues: 89 loop : -0.48 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 PHE 0.023 0.001 PHE R 79 TYR 0.012 0.001 TYR I 12 ARG 0.003 0.000 ARG K 13 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 943) hydrogen bonds : angle 4.16504 ( 2788) covalent geometry : bond 0.00281 (12505) covalent geometry : angle 0.51834 (16907) *********************** 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 235 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.188 Fit side-chains REVERT: 1 66 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5594 (tmm) REVERT: 3 25 ILE cc_start: 0.8684 (mt) cc_final: 0.8412 (mp) REVERT: 4 69 PHE cc_start: 0.6742 (m-80) cc_final: 0.5480 (t80) REVERT: 5 38 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7926 (mtt-85) REVERT: 5 75 MET cc_start: 0.3999 (mtp) cc_final: 0.3525 (mtt) REVERT: 7 75 MET cc_start: 0.7592 (mtm) cc_final: 0.7259 (pmm) REVERT: G 75 ARG cc_start: 0.7377 (mtp85) cc_final: 0.5709 (ptt90) REVERT: G 147 GLU cc_start: 0.7545 (mp0) cc_final: 0.7148 (mm-30) REVERT: G 154 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7031 (mm-30) REVERT: G 195 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: I 36 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: K 7 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8187 (tp30) REVERT: N 147 ILE cc_start: 0.7956 (mt) cc_final: 0.7701 (pt) REVERT: N 181 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6420 (tpp) REVERT: N 199 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7925 (tt) REVERT: S 85 TRP cc_start: 0.8033 (OUTLIER) cc_final: 0.6333 (m-90) REVERT: T 32 TYR cc_start: 0.6684 (m-10) cc_final: 0.6482 (m-10) outliers start: 32 outliers final: 10 residues processed: 217 average time/residue: 1.1986 time to fit residues: 283.2495 Evaluate side-chains 222 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 I residue 29 THR Chi-restraints excluded: chain I residue 36 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 92 optimal weight: 0.0570 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 141 optimal weight: 0.0670 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN N 56 GLN P 8 ASN R 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.149400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.109451 restraints weight = 29496.419| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.62 r_work: 0.3173 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12505 Z= 0.119 Angle : 0.510 10.925 16907 Z= 0.265 Chirality : 0.040 0.170 1978 Planarity : 0.003 0.039 2080 Dihedral : 9.360 146.506 1842 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.07 % Allowed : 16.97 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.21), residues: 1560 helix: 2.35 (0.15), residues: 1097 sheet: 0.03 (0.54), residues: 85 loop : -0.36 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 10 HIS 0.002 0.000 HIS H 66 PHE 0.024 0.001 PHE R 79 TYR 0.009 0.001 TYR G 193 ARG 0.003 0.000 ARG H 34 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 943) hydrogen bonds : angle 4.08759 ( 2788) covalent geometry : bond 0.00234 (12505) covalent geometry : angle 0.51035 (16907) *********************** 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: 25 poor density : 210 time to evaluate : 1.257 Fit side-chains REVERT: 1 66 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5545 (tmm) REVERT: 3 25 ILE cc_start: 0.8629 (mt) cc_final: 0.8367 (mp) REVERT: 4 69 PHE cc_start: 0.6649 (m-80) cc_final: 0.5420 (t80) REVERT: 5 75 MET cc_start: 0.4033 (mtp) cc_final: 0.3600 (mtt) REVERT: 7 75 MET cc_start: 0.7525 (mtm) cc_final: 0.7289 (pmm) REVERT: G 75 ARG cc_start: 0.7347 (mtp85) cc_final: 0.5722 (ptt90) REVERT: G 130 GLU cc_start: 0.8210 (mm-30) cc_final: 0.8008 (mm-30) REVERT: G 147 GLU cc_start: 0.7426 (mp0) cc_final: 0.6990 (mm-30) REVERT: G 154 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6978 (mm-30) REVERT: G 195 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: K 7 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8109 (tp30) REVERT: N 56 GLN cc_start: 0.8206 (tp40) cc_final: 0.7892 (mm-40) REVERT: N 147 ILE cc_start: 0.7989 (mt) cc_final: 0.7724 (pt) REVERT: N 181 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6599 (tpp) REVERT: N 199 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7851 (tt) REVERT: S 85 TRP cc_start: 0.7990 (OUTLIER) cc_final: 0.6259 (m-90) outliers start: 25 outliers final: 7 residues processed: 220 average time/residue: 1.2179 time to fit residues: 291.4783 Evaluate side-chains 211 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN N 4 ASN P 8 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.106860 restraints weight = 25208.233| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.43 r_work: 0.3147 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2336 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= 0.140 Angle : 0.536 11.266 16907 Z= 0.277 Chirality : 0.041 0.195 1978 Planarity : 0.004 0.039 2080 Dihedral : 9.373 147.417 1842 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.99 % Allowed : 17.85 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1560 helix: 2.28 (0.15), residues: 1102 sheet: 0.04 (0.54), residues: 89 loop : -0.42 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 PHE 0.023 0.001 PHE R 79 TYR 0.020 0.001 TYR T 32 ARG 0.002 0.000 ARG K 13 Details of bonding type rmsd hydrogen bonds : bond 0.04972 ( 943) hydrogen bonds : angle 4.12524 ( 2788) covalent geometry : bond 0.00302 (12505) covalent geometry : angle 0.53613 (16907) *********************** 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 224 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 1.205 Fit side-chains REVERT: 1 66 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5563 (tmm) REVERT: 3 25 ILE cc_start: 0.8710 (mt) cc_final: 0.8444 (mp) REVERT: 4 69 PHE cc_start: 0.6632 (m-80) cc_final: 0.5386 (t80) REVERT: 5 75 MET cc_start: 0.4058 (mtp) cc_final: 0.3566 (mtt) REVERT: 7 75 MET cc_start: 0.7577 (mtm) cc_final: 0.7254 (pmm) REVERT: G 75 ARG cc_start: 0.7329 (mtp85) cc_final: 0.5669 (ptt180) REVERT: G 147 GLU cc_start: 0.7512 (mp0) cc_final: 0.7123 (mm-30) REVERT: G 154 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: I 32 LYS cc_start: 0.6228 (tttt) cc_final: 0.5907 (tttm) REVERT: I 37 LYS cc_start: 0.8544 (ttmt) cc_final: 0.7816 (tmtt) REVERT: K 7 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8265 (tp30) REVERT: N 147 ILE cc_start: 0.7974 (mt) cc_final: 0.7670 (pt) REVERT: N 181 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6523 (tpp) REVERT: N 199 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7885 (tt) REVERT: S 85 TRP cc_start: 0.8022 (OUTLIER) cc_final: 0.6309 (m-90) outliers start: 24 outliers final: 10 residues processed: 211 average time/residue: 1.1390 time to fit residues: 262.6789 Evaluate side-chains 214 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 154 GLU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 136 GLU 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 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 18 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 129 GLN N 4 ASN N 56 GLN P 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.105649 restraints weight = 30018.050| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.65 r_work: 0.3128 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2317 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= 0.146 Angle : 0.546 11.780 16907 Z= 0.282 Chirality : 0.041 0.183 1978 Planarity : 0.003 0.038 2080 Dihedral : 9.368 147.010 1842 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.75 % Allowed : 18.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.21), residues: 1560 helix: 2.28 (0.15), residues: 1099 sheet: 0.03 (0.54), residues: 89 loop : -0.38 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 PHE 0.024 0.001 PHE R 79 TYR 0.013 0.001 TYR I 12 ARG 0.003 0.000 ARG K 13 Details of bonding type rmsd hydrogen bonds : bond 0.05031 ( 943) hydrogen bonds : angle 4.17043 ( 2788) covalent geometry : bond 0.00320 (12505) covalent geometry : angle 0.54561 (16907) ********************** 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 217 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.371 Fit side-chains REVERT: 1 66 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5566 (tmm) REVERT: 3 25 ILE cc_start: 0.8604 (mt) cc_final: 0.8360 (mp) REVERT: 4 69 PHE cc_start: 0.6647 (m-80) cc_final: 0.5422 (t80) REVERT: 5 75 MET cc_start: 0.4093 (mtp) cc_final: 0.3609 (mtt) REVERT: 7 75 MET cc_start: 0.7526 (mtm) cc_final: 0.7236 (pmm) REVERT: G 75 ARG cc_start: 0.7224 (mtp85) cc_final: 0.5648 (ptt180) REVERT: G 147 GLU cc_start: 0.7405 (mp0) cc_final: 0.7018 (mm-30) REVERT: G 154 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: G 195 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: I 37 LYS cc_start: 0.8581 (ttmt) cc_final: 0.7842 (tmtt) REVERT: N 147 ILE cc_start: 0.8021 (mt) cc_final: 0.7693 (pt) REVERT: N 181 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6514 (tpp) REVERT: N 199 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7814 (tt) REVERT: S 85 TRP cc_start: 0.7980 (OUTLIER) cc_final: 0.6196 (m-90) outliers start: 21 outliers final: 11 residues processed: 205 average time/residue: 1.1583 time to fit residues: 259.4571 Evaluate side-chains 212 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain M residue 141 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 145 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 129 GLN N 4 ASN N 56 GLN P 8 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106682 restraints weight = 20709.432| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.19 r_work: 0.3149 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2318 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= 0.147 Angle : 0.548 12.088 16907 Z= 0.283 Chirality : 0.041 0.194 1978 Planarity : 0.004 0.038 2080 Dihedral : 9.362 147.318 1842 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.91 % Allowed : 18.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.21), residues: 1560 helix: 2.25 (0.15), residues: 1100 sheet: -0.01 (0.54), residues: 89 loop : -0.37 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 10 HIS 0.004 0.001 HIS H 51 PHE 0.023 0.001 PHE R 79 TYR 0.014 0.001 TYR I 12 ARG 0.003 0.000 ARG K 13 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 943) hydrogen bonds : angle 4.18323 ( 2788) covalent geometry : bond 0.00325 (12505) covalent geometry : angle 0.54835 (16907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12665.72 seconds wall clock time: 223 minutes 12.10 seconds (13392.10 seconds total)