Starting phenix.real_space_refine on Fri Jul 3 07:10:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h9f_34565/07_2026/8h9f_34565.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9f_34565/07_2026/8h9f_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_2026/8h9f_34565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2026/8h9f_34565.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2026/8h9f_34565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2026/8h9f_34565.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2026/8h9f_34565.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h9f_34565/07_2026/8h9f_34565.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 63 5.16 5 C 8059 2.51 5 N 1938 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12265 Number of models: 1 Model: "" Number of chains: 22 Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "3" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 534 Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1485 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 30} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'3PH': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Time building chain proxies: 2.53, per 1000 atoms: 0.21 Number of scatterers: 12265 At special positions: 0 Unit cell: (112.42, 104.39, 137.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 5 15.00 O 2200 8.00 N 1938 7.00 C 8059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 569.1 milliseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 5 sheets defined 77.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain '1' and resid 2 through 15 Processing helix chain '1' and resid 17 through 39 removed outlier: 4.276A pdb=" N SER 1 21 " --> pdb=" O GLY 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 73 removed outlier: 3.516A pdb=" N ALA 1 59 " --> pdb=" O ALA 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 16 Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 removed outlier: 3.610A pdb=" N ALA 2 59 " --> pdb=" O ALA 2 55 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 2 61 " --> pdb=" O SER 2 57 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 17 removed outlier: 4.040A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 removed outlier: 3.517A pdb=" N ALA 3 59 " --> pdb=" O ALA 3 55 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY 3 61 " --> pdb=" O SER 3 57 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 16 Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 removed outlier: 3.850A pdb=" N CYS 4 64 " --> pdb=" O MET 4 60 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL 4 67 " --> pdb=" O PHE 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 16 Processing helix chain '5' and resid 17 through 39 removed outlier: 4.427A pdb=" N SER 5 21 " --> pdb=" O GLY 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 73 removed outlier: 3.679A pdb=" N GLU 5 58 " --> pdb=" O PHE 5 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 5 59 " --> pdb=" O ALA 5 55 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 17 removed outlier: 4.045A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 39 removed outlier: 4.428A pdb=" N SER 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 16 Processing helix chain '7' and resid 17 through 39 removed outlier: 4.404A pdb=" N SER 7 21 " --> pdb=" O GLY 7 17 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 73 removed outlier: 3.553A pdb=" N PHE 7 73 " --> pdb=" O PHE 7 69 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 17 removed outlier: 3.984A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 removed outlier: 3.550A pdb=" N ALA 8 59 " --> pdb=" O ALA 8 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE 8 73 " --> pdb=" O PHE 8 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 49 removed outlier: 3.979A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix removed outlier: 3.655A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 98 Processing helix chain 'G' and resid 109 through 118 removed outlier: 3.690A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.552A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 187 through 193 removed outlier: 3.540A pdb=" N SER G 191 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.687A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 8 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.296A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.615A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 97 removed outlier: 3.891A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 140 through 143 removed outlier: 3.524A pdb=" N LYS M 143 " --> pdb=" O PRO M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'N' and resid 6 through 10 removed outlier: 3.645A pdb=" N ILE N 10 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.641A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 85 removed outlier: 3.670A pdb=" N THR N 81 " --> pdb=" O ILE N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 3.881A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.003A pdb=" N PHE N 128 " --> pdb=" O ALA N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 138 removed outlier: 3.513A pdb=" N LEU N 137 " --> pdb=" O PRO N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 181 removed outlier: 3.559A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) Proline residue: N 153 - end of helix Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'P' and resid 4 through 9 Processing helix chain 'P' and resid 9 through 19 removed outlier: 3.598A pdb=" N MET P 13 " --> pdb=" O ILE P 9 " (cutoff:3.500A) Proline residue: P 15 - end of helix removed outlier: 3.552A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 Processing helix chain 'Q' and resid 1 through 7 removed outlier: 5.605A pdb=" N THR Q 6 " --> pdb=" O GLN Q 3 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR Q 7 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 22 removed outlier: 3.533A pdb=" N MET Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 30 removed outlier: 3.657A pdb=" N ASN Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.749A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 79 removed outlier: 4.387A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.694A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU S 36 " --> pdb=" O TYR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 68 through 93 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 3.861A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.113A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA G 127 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 5.216A pdb=" N ASN H 29 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N PHE H 20 " --> pdb=" O ASN H 29 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY H 80 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.286A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'N' and resid 13 through 14 949 hydrogen bonds defined for protein. 2788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.55 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 - 16.54: 6625 16.54 - 33.07: 569 33.07 - 49.61: 126 49.61 - 66.15: 38 66.15 - 82.68: 10 Dihedral angle restraints: 7368 sinusoidal: 2822 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=" CA ARG N 118 " pdb=" C ARG N 118 " pdb=" N SER N 119 " pdb=" CA SER N 119 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 7365 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: 12.350 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.950 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 13.847 82.681 4468 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.16 % Allowed : 2.87 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.19), residues: 1560 helix: -1.16 (0.14), residues: 1115 sheet: -0.87 (0.54), residues: 88 loop : -2.48 (0.28), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 13 TYR 0.015 0.001 TYR I 12 PHE 0.019 0.002 PHE 8 29 TRP 0.013 0.001 TRP P 10 HIS 0.004 0.001 HIS G 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.27 (12505) covalent geometry : angle 0.68859 / 0.40 (16907) hydrogen bonds : bond 0.14327 / 9.75 ( 943) hydrogen bonds : angle 6.99351 / 5.16 ( 2788) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.503 Fit side-chains REVERT: 4 69 PHE cc_start: 0.7614 (m-80) cc_final: 0.6829 (t80) REVERT: 5 75 MET cc_start: 0.4321 (mtp) cc_final: 0.3877 (mtt) REVERT: 6 7 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7635 (mttp) REVERT: 8 60 MET cc_start: 0.7882 (mmm) cc_final: 0.7360 (mmp) REVERT: G 64 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7394 (mmmt) REVERT: G 75 ARG cc_start: 0.7588 (mtp85) cc_final: 0.6779 (ptt180) REVERT: Q 28 MET cc_start: 0.8342 (mmp) cc_final: 0.7775 (mmp) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.5334 time to fit residues: 136.3720 Evaluate side-chains 205 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 44 GLN G 120 HIS G 163 ASN H 15 GLN H 85 ASN H 111 ASN H 132 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109145 restraints weight = 28172.593| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.89 r_work: 0.3083 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1295 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= 0.153 Angle : 0.563 6.510 16907 Z= 0.301 Chirality : 0.041 0.178 1978 Planarity : 0.004 0.039 2080 Dihedral : 8.672 58.853 1793 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.47 % Allowed : 10.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1560 helix: 0.76 (0.15), residues: 1109 sheet: -0.72 (0.55), residues: 91 loop : -1.62 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 13 TYR 0.011 0.001 TYR I 12 PHE 0.022 0.002 PHE R 79 TRP 0.017 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (12505) covalent geometry : angle 0.56335 / 0.30 (16907) hydrogen bonds : bond 0.05732 / 3.87 ( 943) hydrogen bonds : angle 4.71180 / 3.49 ( 2788) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.481 Fit side-chains REVERT: 2 75 MET cc_start: 0.4400 (tpt) cc_final: 0.4177 (ttm) REVERT: 4 69 PHE cc_start: 0.6909 (m-80) cc_final: 0.5583 (t80) REVERT: 5 75 MET cc_start: 0.4133 (mtp) cc_final: 0.3582 (mtt) REVERT: 6 7 LYS cc_start: 0.7108 (mtmt) cc_final: 0.6561 (mttp) REVERT: 8 60 MET cc_start: 0.7193 (mmm) cc_final: 0.6953 (mmp) REVERT: G 64 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6644 (mmmt) REVERT: G 75 ARG cc_start: 0.7361 (mtp85) cc_final: 0.5801 (ptt180) REVERT: G 130 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7926 (mt-10) REVERT: G 147 GLU cc_start: 0.7615 (mp0) cc_final: 0.7257 (mm-30) REVERT: I 7 GLN cc_start: 0.7241 (mm110) cc_final: 0.6958 (mt0) REVERT: I 36 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: N 56 GLN cc_start: 0.8264 (tp40) cc_final: 0.7960 (mm-40) REVERT: N 199 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7915 (tt) REVERT: Q 28 MET cc_start: 0.8690 (mmp) cc_final: 0.8372 (mmp) REVERT: R 91 LYS cc_start: 0.7372 (tmmt) cc_final: 0.7144 (tmmt) outliers start: 30 outliers final: 8 residues processed: 228 average time/residue: 0.5640 time to fit residues: 139.6169 Evaluate side-chains 214 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 3 residue 51 ILE Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 36 GLU 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 12 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 139 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3710 r_free = 0.3710 target = 0.145060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106519 restraints weight = 23801.977| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.28 r_work: 0.3135 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1641 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= 0.144 Angle : 0.529 8.021 16907 Z= 0.281 Chirality : 0.041 0.207 1978 Planarity : 0.004 0.038 2080 Dihedral : 8.217 59.924 1793 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.39 % Allowed : 13.63 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1560 helix: 1.52 (0.15), residues: 1109 sheet: -0.55 (0.54), residues: 91 loop : -1.16 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 13 TYR 0.011 0.001 TYR I 12 PHE 0.025 0.001 PHE S 86 TRP 0.012 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12505) covalent geometry : angle 0.52918 / 0.28 (16907) hydrogen bonds : bond 0.05374 / 3.61 ( 943) hydrogen bonds : angle 4.42257 / 3.27 ( 2788) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.534 Fit side-chains REVERT: 1 60 MET cc_start: 0.6953 (mmp) cc_final: 0.6697 (mmt) REVERT: 4 69 PHE cc_start: 0.6909 (m-80) cc_final: 0.5580 (t80) REVERT: 5 38 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7902 (mtt-85) REVERT: 5 75 MET cc_start: 0.4125 (mtp) cc_final: 0.3571 (mtt) REVERT: 6 7 LYS cc_start: 0.7107 (mtmt) cc_final: 0.6575 (mttp) REVERT: G 35 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: G 64 LYS cc_start: 0.7455 (mmtt) cc_final: 0.6673 (mmmt) REVERT: G 75 ARG cc_start: 0.7400 (mtp85) cc_final: 0.5776 (ptt180) REVERT: G 147 GLU cc_start: 0.7681 (mp0) cc_final: 0.7299 (mm-30) REVERT: G 154 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6967 (mm-30) REVERT: G 195 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: H 32 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7622 (m-40) REVERT: K 7 GLU cc_start: 0.8371 (tt0) cc_final: 0.8046 (tp30) REVERT: K 83 ASP cc_start: 0.8127 (m-30) cc_final: 0.7920 (m-30) REVERT: N 56 GLN cc_start: 0.8301 (tp40) cc_final: 0.7993 (mm-40) REVERT: N 181 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6417 (tpp) REVERT: Q 28 MET cc_start: 0.8730 (mmp) cc_final: 0.8453 (mmp) REVERT: S 94 LYS cc_start: 0.6857 (pttp) cc_final: 0.6629 (pttp) outliers start: 29 outliers final: 6 residues processed: 224 average time/residue: 0.5547 time to fit residues: 135.4813 Evaluate side-chains 217 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 H residue 32 ASN Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 39 SER 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 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3719 r_free = 0.3719 target = 0.145870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109833 restraints weight = 18837.895| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.98 r_work: 0.3155 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- 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 = 0.42 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1825 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= 0.141 Angle : 0.519 7.836 16907 Z= 0.274 Chirality : 0.041 0.192 1978 Planarity : 0.004 0.037 2080 Dihedral : 7.871 56.984 1793 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.79 % Allowed : 14.34 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1560 helix: 1.86 (0.15), residues: 1103 sheet: -0.42 (0.54), residues: 91 loop : -0.83 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 13 TYR 0.010 0.001 TYR I 12 PHE 0.024 0.001 PHE R 79 TRP 0.010 0.001 TRP R 28 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12505) covalent geometry : angle 0.51874 / 0.27 (16907) hydrogen bonds : bond 0.05199 / 3.49 ( 943) hydrogen bonds : angle 4.30912 / 3.19 ( 2788) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.503 Fit side-chains REVERT: 4 69 PHE cc_start: 0.6877 (m-80) cc_final: 0.5620 (t80) REVERT: 5 38 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7898 (mtt-85) REVERT: 5 75 MET cc_start: 0.4044 (mtp) cc_final: 0.3546 (mtt) REVERT: G 35 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8328 (tm-30) REVERT: G 64 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6586 (mmmt) REVERT: G 75 ARG cc_start: 0.7416 (mtp85) cc_final: 0.5820 (ptt180) REVERT: G 130 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7968 (mm-30) REVERT: G 147 GLU cc_start: 0.7634 (mp0) cc_final: 0.7191 (mm-30) REVERT: G 154 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: G 195 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7968 (m-30) REVERT: K 7 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: K 83 ASP cc_start: 0.8117 (m-30) cc_final: 0.7906 (m-30) REVERT: N 56 GLN cc_start: 0.8289 (tp40) cc_final: 0.7996 (mm-40) REVERT: N 181 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6344 (tpp) REVERT: N 199 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7920 (tt) REVERT: S 84 MET cc_start: 0.7278 (mmp) cc_final: 0.7064 (mmp) outliers start: 34 outliers final: 10 residues processed: 219 average time/residue: 0.5546 time to fit residues: 131.7090 Evaluate side-chains 218 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 H residue 34 ARG Chi-restraints excluded: chain H residue 127 THR 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 P residue 30 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103068 restraints weight = 22158.371| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.31 r_work: 0.3097 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12505 Z= 0.194 Angle : 0.563 8.357 16907 Z= 0.296 Chirality : 0.043 0.187 1978 Planarity : 0.004 0.038 2080 Dihedral : 7.733 56.936 1793 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.51 % Allowed : 14.90 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.21), residues: 1560 helix: 1.79 (0.15), residues: 1110 sheet: -0.37 (0.54), residues: 89 loop : -0.85 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 41 TYR 0.016 0.001 TYR G 193 PHE 0.024 0.002 PHE R 79 TRP 0.011 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (12505) covalent geometry : angle 0.56275 / 0.30 (16907) hydrogen bonds : bond 0.05761 / 3.89 ( 943) hydrogen bonds : angle 4.38202 / 3.25 ( 2788) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 207 time to evaluate : 0.489 Fit side-chains REVERT: 1 60 MET cc_start: 0.7066 (mmt) cc_final: 0.6856 (mmt) REVERT: 4 69 PHE cc_start: 0.6873 (m-80) cc_final: 0.5612 (t80) REVERT: 5 75 MET cc_start: 0.4130 (mtp) cc_final: 0.3602 (mtt) REVERT: 6 7 LYS cc_start: 0.7110 (mtmt) cc_final: 0.6554 (mttp) REVERT: G 35 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: G 75 ARG cc_start: 0.7388 (mtp85) cc_final: 0.5722 (ptt180) REVERT: G 147 GLU cc_start: 0.7607 (mp0) cc_final: 0.7228 (mm-30) REVERT: G 154 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7075 (mm-30) REVERT: G 195 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8062 (m-30) REVERT: H 146 GLU cc_start: 0.5840 (tp30) cc_final: 0.5640 (mt-10) REVERT: K 7 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8080 (tp30) REVERT: K 14 TYR cc_start: 0.8831 (m-80) cc_final: 0.8586 (m-80) REVERT: K 83 ASP cc_start: 0.8125 (m-30) cc_final: 0.7913 (m-30) REVERT: N 181 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6388 (tpp) REVERT: N 199 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7885 (tt) REVERT: Q 28 MET cc_start: 0.8692 (mmp) cc_final: 0.8409 (mmp) REVERT: R 44 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7202 (mt0) REVERT: S 84 MET cc_start: 0.7314 (mmp) cc_final: 0.7094 (mmp) REVERT: T 32 TYR cc_start: 0.6679 (m-10) cc_final: 0.6443 (m-10) outliers start: 43 outliers final: 17 residues processed: 227 average time/residue: 0.5721 time to fit residues: 141.4178 Evaluate side-chains 230 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 G residue 35 GLU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 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 P residue 30 LEU Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain R residue 44 GLN 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 67 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 GLN Q 5 ASN R 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105236 restraints weight = 20601.858| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.23 r_work: 0.3126 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1927 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= 0.144 Angle : 0.527 8.747 16907 Z= 0.278 Chirality : 0.041 0.168 1978 Planarity : 0.004 0.037 2080 Dihedral : 7.507 58.257 1793 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.87 % Allowed : 16.02 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.21), residues: 1560 helix: 2.02 (0.15), residues: 1104 sheet: -0.30 (0.53), residues: 89 loop : -0.66 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 128 TYR 0.013 0.001 TYR G 193 PHE 0.024 0.001 PHE R 79 TRP 0.010 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (12505) covalent geometry : angle 0.52747 / 0.28 (16907) hydrogen bonds : bond 0.05280 / 3.55 ( 943) hydrogen bonds : angle 4.29268 / 3.19 ( 2788) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.457 Fit side-chains REVERT: 4 69 PHE cc_start: 0.6813 (m-80) cc_final: 0.5554 (t80) REVERT: 5 38 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7926 (mtt-85) REVERT: 5 75 MET cc_start: 0.4099 (mtp) cc_final: 0.3570 (mtt) REVERT: 7 75 MET cc_start: 0.7551 (mtm) cc_final: 0.7225 (pmm) REVERT: G 75 ARG cc_start: 0.7399 (mtp85) cc_final: 0.5743 (ptt180) REVERT: G 147 GLU cc_start: 0.7587 (mp0) cc_final: 0.7143 (mm-30) REVERT: G 154 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: G 175 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7769 (mt-10) REVERT: G 195 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: H 32 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7717 (m-40) REVERT: H 146 GLU cc_start: 0.5793 (tp30) cc_final: 0.5532 (mm-30) REVERT: K 7 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: K 14 TYR cc_start: 0.8824 (m-80) cc_final: 0.8585 (m-80) REVERT: N 143 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7239 (mp) REVERT: N 181 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6432 (tpp) REVERT: N 199 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7817 (tt) REVERT: R 44 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7262 (mt0) REVERT: S 85 TRP cc_start: 0.7997 (OUTLIER) cc_final: 0.6316 (m-90) REVERT: T 32 TYR cc_start: 0.6653 (m-10) cc_final: 0.6452 (m-10) outliers start: 35 outliers final: 16 residues processed: 222 average time/residue: 0.5676 time to fit residues: 137.1966 Evaluate side-chains 221 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 5 residue 18 VAL Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain N residue 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 P residue 30 LEU Chi-restraints excluded: chain R residue 44 GLN Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106698 restraints weight = 20693.826| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.18 r_work: 0.3145 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12505 Z= 0.137 Angle : 0.524 9.132 16907 Z= 0.275 Chirality : 0.041 0.176 1978 Planarity : 0.004 0.037 2080 Dihedral : 7.313 59.502 1793 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.03 % Allowed : 16.10 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.21), residues: 1560 helix: 2.11 (0.15), residues: 1103 sheet: -0.41 (0.53), residues: 89 loop : -0.54 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 128 TYR 0.012 0.001 TYR G 193 PHE 0.023 0.001 PHE R 79 TRP 0.009 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (12505) covalent geometry : angle 0.52403 / 0.27 (16907) hydrogen bonds : bond 0.05107 / 3.43 ( 943) hydrogen bonds : angle 4.23272 / 3.14 ( 2788) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.414 Fit side-chains REVERT: 1 66 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5618 (tmm) REVERT: 3 25 ILE cc_start: 0.8670 (mt) cc_final: 0.8391 (mp) REVERT: 4 69 PHE cc_start: 0.6768 (m-80) cc_final: 0.5544 (t80) REVERT: 5 38 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7911 (mtt-85) REVERT: 5 75 MET cc_start: 0.4064 (mtp) cc_final: 0.3546 (mtt) REVERT: 7 75 MET cc_start: 0.7594 (mtm) cc_final: 0.7298 (pmm) REVERT: G 75 ARG cc_start: 0.7383 (mtp85) cc_final: 0.5778 (ptt180) REVERT: G 147 GLU cc_start: 0.7534 (mp0) cc_final: 0.7134 (mm-30) REVERT: G 154 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: G 195 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: H 32 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7690 (m-40) REVERT: I 37 LYS cc_start: 0.8589 (ttmt) cc_final: 0.7880 (tmtt) REVERT: K 7 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: N 181 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6372 (tpp) REVERT: N 199 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7813 (tt) REVERT: S 85 TRP cc_start: 0.7988 (OUTLIER) cc_final: 0.6284 (m-90) REVERT: T 32 TYR cc_start: 0.6644 (m-10) cc_final: 0.6440 (m-10) outliers start: 37 outliers final: 13 residues processed: 221 average time/residue: 0.5299 time to fit residues: 127.6817 Evaluate side-chains 219 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 136 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 145 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 137 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.105901 restraints weight = 28376.111| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.57 r_work: 0.3136 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2160 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 : 0.528 10.432 16907 Z= 0.274 Chirality : 0.040 0.189 1978 Planarity : 0.004 0.039 2080 Dihedral : 7.020 59.222 1793 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.31 % Allowed : 17.05 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.21), residues: 1560 helix: 2.18 (0.15), residues: 1102 sheet: -0.33 (0.53), residues: 89 loop : -0.48 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 128 TYR 0.012 0.001 TYR I 12 PHE 0.023 0.001 PHE R 79 TRP 0.009 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (12505) covalent geometry : angle 0.52798 / 0.27 (16907) hydrogen bonds : bond 0.04975 / 3.34 ( 943) hydrogen bonds : angle 4.18913 / 3.11 ( 2788) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.456 Fit side-chains REVERT: 1 66 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5639 (tmm) REVERT: 3 25 ILE cc_start: 0.8664 (mt) cc_final: 0.8389 (mp) REVERT: 4 69 PHE cc_start: 0.6754 (m-80) cc_final: 0.5464 (t80) REVERT: 5 38 ARG cc_start: 0.8155 (mtt180) cc_final: 0.7932 (mtt-85) REVERT: 5 75 MET cc_start: 0.4050 (mtp) cc_final: 0.3536 (mtt) REVERT: 7 75 MET cc_start: 0.7560 (mtm) cc_final: 0.7325 (pmm) REVERT: G 75 ARG cc_start: 0.7382 (mtp85) cc_final: 0.5773 (ptt180) REVERT: G 147 GLU cc_start: 0.7524 (mp0) cc_final: 0.7165 (mm-30) REVERT: G 154 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: G 195 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: I 32 LYS cc_start: 0.6220 (tttt) cc_final: 0.5911 (tttm) REVERT: I 37 LYS cc_start: 0.8524 (ttmt) cc_final: 0.7835 (tmtt) REVERT: K 7 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: K 14 TYR cc_start: 0.8754 (m-80) cc_final: 0.8507 (m-80) REVERT: N 56 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7903 (mm-40) REVERT: N 181 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6430 (tpp) REVERT: N 199 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7872 (tt) REVERT: S 85 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.6292 (m-90) REVERT: T 32 TYR cc_start: 0.6718 (m-10) cc_final: 0.6508 (m-10) outliers start: 28 outliers final: 11 residues processed: 220 average time/residue: 0.4983 time to fit residues: 119.7710 Evaluate side-chains 212 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 144 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 159 ASN 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 = 0.3723 r_free = 0.3723 target = 0.146354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106680 restraints weight = 28387.304| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.61 r_work: 0.3145 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12505 Z= 0.128 Angle : 0.524 10.763 16907 Z= 0.272 Chirality : 0.040 0.180 1978 Planarity : 0.003 0.039 2080 Dihedral : 6.786 59.608 1793 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.31 % Allowed : 17.37 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.21), residues: 1560 helix: 2.25 (0.15), residues: 1103 sheet: -0.24 (0.53), residues: 89 loop : -0.41 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 128 TYR 0.011 0.001 TYR G 193 PHE 0.023 0.001 PHE R 79 TRP 0.008 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (12505) covalent geometry : angle 0.52429 / 0.27 (16907) hydrogen bonds : bond 0.04865 / 3.27 ( 943) hydrogen bonds : angle 4.14562 / 3.08 ( 2788) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.506 Fit side-chains REVERT: 1 66 MET cc_start: 0.6043 (OUTLIER) cc_final: 0.5549 (tmm) REVERT: 3 25 ILE cc_start: 0.8586 (mt) cc_final: 0.8308 (mp) REVERT: 4 69 PHE cc_start: 0.6653 (m-80) cc_final: 0.5397 (t80) REVERT: 5 38 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7846 (mtt-85) REVERT: 5 75 MET cc_start: 0.4062 (mtp) cc_final: 0.3573 (mtt) REVERT: G 75 ARG cc_start: 0.7319 (mtp85) cc_final: 0.5762 (ptt180) REVERT: G 147 GLU cc_start: 0.7400 (mp0) cc_final: 0.7042 (mm-30) REVERT: G 154 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7056 (mm-30) REVERT: G 195 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: K 7 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: K 14 TYR cc_start: 0.8736 (m-80) cc_final: 0.8487 (m-80) REVERT: N 56 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7839 (mm-40) REVERT: N 181 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6474 (tpp) REVERT: N 199 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7801 (tt) REVERT: S 85 TRP cc_start: 0.7970 (OUTLIER) cc_final: 0.6197 (m-90) outliers start: 28 outliers final: 11 residues processed: 211 average time/residue: 0.5173 time to fit residues: 119.1211 Evaluate side-chains 213 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 88 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3699 r_free = 0.3699 target = 0.144246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.105278 restraints weight = 22029.634| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.26 r_work: 0.3127 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12505 Z= 0.161 Angle : 0.560 11.803 16907 Z= 0.290 Chirality : 0.042 0.196 1978 Planarity : 0.004 0.038 2080 Dihedral : 6.813 59.650 1793 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.67 % Allowed : 17.85 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.21), residues: 1560 helix: 2.17 (0.15), residues: 1103 sheet: -0.13 (0.53), residues: 89 loop : -0.44 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 128 TYR 0.019 0.001 TYR T 32 PHE 0.023 0.001 PHE R 79 TRP 0.008 0.001 TRP R 28 HIS 0.004 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (12505) covalent geometry : angle 0.56000 / 0.29 (16907) hydrogen bonds : bond 0.05263 / 3.55 ( 943) hydrogen bonds : angle 4.22748 / 3.14 ( 2788) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.451 Fit side-chains REVERT: 3 25 ILE cc_start: 0.8686 (mt) cc_final: 0.8422 (mp) REVERT: 4 69 PHE cc_start: 0.6713 (m-80) cc_final: 0.5465 (t80) REVERT: 5 38 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7939 (mtt-85) REVERT: 5 75 MET cc_start: 0.4116 (mtp) cc_final: 0.3574 (mtt) REVERT: G 75 ARG cc_start: 0.7381 (mtp85) cc_final: 0.5736 (ptt180) REVERT: G 147 GLU cc_start: 0.7513 (mp0) cc_final: 0.7126 (mm-30) REVERT: G 154 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7126 (mm-30) REVERT: G 195 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: I 37 LYS cc_start: 0.8545 (ttmt) cc_final: 0.7831 (tmtt) REVERT: K 7 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8242 (tp30) REVERT: K 14 TYR cc_start: 0.8787 (m-80) cc_final: 0.8519 (m-80) REVERT: N 181 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6511 (tpp) REVERT: N 199 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7900 (tt) REVERT: S 85 TRP cc_start: 0.8041 (OUTLIER) cc_final: 0.6249 (m-90) outliers start: 20 outliers final: 10 residues processed: 210 average time/residue: 0.5165 time to fit residues: 118.2379 Evaluate side-chains 218 residues out of total 1253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 66 MET Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 41 SER Chi-restraints excluded: chain 6 residue 66 MET Chi-restraints excluded: chain 7 residue 41 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 29 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain K residue 7 GLU Chi-restraints excluded: chain N residue 39 ASN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 199 LEU Chi-restraints excluded: chain S residue 85 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 84 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 101 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 129 GLN N 4 ASN P 8 ASN Q 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107240 restraints weight = 24545.376| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.39 r_work: 0.3152 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12505 Z= 0.131 Angle : 0.536 11.863 16907 Z= 0.277 Chirality : 0.041 0.179 1978 Planarity : 0.003 0.038 2080 Dihedral : 6.640 59.827 1793 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.91 % Allowed : 17.77 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.21), residues: 1560 helix: 2.27 (0.15), residues: 1094 sheet: -0.22 (0.53), residues: 89 loop : -0.36 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 34 TYR 0.012 0.001 TYR G 193 PHE 0.023 0.001 PHE R 79 TRP 0.008 0.001 TRP P 10 HIS 0.003 0.001 HIS H 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12505) covalent geometry : angle 0.53614 / 0.28 (16907) hydrogen bonds : bond 0.04891 / 3.29 ( 943) hydrogen bonds : angle 4.17160 / 3.11 ( 2788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5533.28 seconds wall clock time: 94 minutes 50.13 seconds (5690.13 seconds total)