Starting phenix.real_space_refine on Wed Aug 5 10:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddm_46776/08_2026/9ddm_46776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddm_46776/08_2026/9ddm_46776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddm_46776/08_2026/9ddm_46776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddm_46776/08_2026/9ddm_46776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddm_46776/08_2026/9ddm_46776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddm_46776/08_2026/9ddm_46776.map" } resolution = 2.94 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 6211 2.51 5 N 1640 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9582 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1745 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain: "B" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1737 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1730 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain: "D" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1698 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1743 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain: "F" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 234 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 245 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "Y" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 251 Classifications: {'peptide': 33} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 30} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Time building chain proxies: 2.33, per 1000 atoms: 0.24 Number of scatterers: 9582 At special positions: 0 Unit cell: (91.3, 87.98, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1690 8.00 N 1640 7.00 C 6211 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: 0.94 Conformation dependent library (CDL) restraints added in 362.2 milliseconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 14 through 57 Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.664A pdb=" N LEU A 76 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.660A pdb=" N ALA A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 removed outlier: 4.506A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 157 removed outlier: 3.663A pdb=" N LEU A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 163 through 223 removed outlier: 3.650A pdb=" N VAL A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Proline residue: A 169 - end of helix removed outlier: 3.683A pdb=" N ILE A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 14 through 58 removed outlier: 4.111A pdb=" N LYS B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.835A pdb=" N GLY B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.887A pdb=" N ASN B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 removed outlier: 3.543A pdb=" N VAL B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 157 Proline residue: B 138 - end of helix removed outlier: 3.576A pdb=" N ALA B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 222 Proline residue: B 169 - end of helix Proline residue: B 187 - end of helix removed outlier: 4.702A pdb=" N ASN B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.634A pdb=" N LEU C 9 " --> pdb=" O ASN C 5 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 57 Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.715A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 97 Processing helix chain 'C' and resid 100 through 124 removed outlier: 3.527A pdb=" N GLY C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 157 removed outlier: 3.892A pdb=" N LEU C 130 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 163 through 184 removed outlier: 3.682A pdb=" N VAL C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.842A pdb=" N ILE C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 223 removed outlier: 3.631A pdb=" N GLN C 197 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 14 through 57 removed outlier: 3.537A pdb=" N LYS D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.516A pdb=" N GLY D 71 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 100 through 124 removed outlier: 3.679A pdb=" N GLU D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 157 removed outlier: 3.767A pdb=" N LEU D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Proline residue: D 138 - end of helix removed outlier: 3.939A pdb=" N ALA D 155 " --> pdb=" O HIS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 223 removed outlier: 3.681A pdb=" N VAL D 167 " --> pdb=" O THR D 163 " (cutoff:3.500A) Proline residue: D 169 - end of helix Proline residue: D 187 - end of helix removed outlier: 4.026A pdb=" N ASN D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 Processing helix chain 'E' and resid 14 through 57 removed outlier: 3.712A pdb=" N ARG E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.907A pdb=" N GLY E 71 " --> pdb=" O GLN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 98 removed outlier: 3.841A pdb=" N ARG E 95 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER E 98 " --> pdb=" O HIS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 124 removed outlier: 4.087A pdb=" N ASN E 122 " --> pdb=" O ARG E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 159 removed outlier: 3.825A pdb=" N LEU E 130 " --> pdb=" O HIS E 126 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 3.888A pdb=" N VAL E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 167 through 225 removed outlier: 3.510A pdb=" N THR E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Proline residue: E 187 - end of helix Processing helix chain 'F' and resid 5 through 32 removed outlier: 3.936A pdb=" N ASP F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 33 Processing helix chain 'Y' and resid 18 through 40 Proline residue: Y 37 - end of helix Processing helix chain 'Z' and resid 19 through 35 removed outlier: 4.184A pdb=" N ASP Z 23 " --> pdb=" O VAL Z 19 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2571 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: 1.69 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2779 1.34 - 1.46: 1407 1.46 - 1.58: 5495 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 9763 Sorted by residual: bond pdb=" N ILE C 186 " pdb=" CA ILE C 186 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" N HIS B 99 " pdb=" CA HIS B 99 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.21e-02 6.83e+03 9.06e+00 bond pdb=" N ASN D 75 " pdb=" CA ASN D 75 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.12e-02 7.97e+03 8.94e+00 bond pdb=" N LYS A 72 " pdb=" CA LYS A 72 " ideal model delta sigma weight residual 1.459 1.486 -0.027 9.10e-03 1.21e+04 8.91e+00 bond pdb=" CZ ARG E 38 " pdb=" NH2 ARG E 38 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.85e+00 ... (remaining 9758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 7844 1.32 - 2.65: 3967 2.65 - 3.97: 1225 3.97 - 5.29: 157 5.29 - 6.62: 10 Bond angle restraints: 13203 Sorted by residual: angle pdb=" C ASP D 8 " pdb=" N LEU D 9 " pdb=" CA LEU D 9 " ideal model delta sigma weight residual 120.54 125.93 -5.39 1.35e+00 5.49e-01 1.60e+01 angle pdb=" CB HIS E 94 " pdb=" CG HIS E 94 " pdb=" CD2 HIS E 94 " ideal model delta sigma weight residual 131.20 126.01 5.19 1.30e+00 5.92e-01 1.60e+01 angle pdb=" C ALA B 185 " pdb=" N ILE B 186 " pdb=" CA ILE B 186 " ideal model delta sigma weight residual 120.43 124.27 -3.84 9.60e-01 1.09e+00 1.60e+01 angle pdb=" OE1 GLN D 37 " pdb=" CD GLN D 37 " pdb=" NE2 GLN D 37 " ideal model delta sigma weight residual 122.60 118.61 3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" OE1 GLN C 165 " pdb=" CD GLN C 165 " pdb=" NE2 GLN C 165 " ideal model delta sigma weight residual 122.60 118.63 3.97 1.00e+00 1.00e+00 1.58e+01 ... (remaining 13198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5382 17.76 - 35.53: 356 35.53 - 53.29: 54 53.29 - 71.05: 22 71.05 - 88.81: 10 Dihedral angle restraints: 5824 sinusoidal: 2287 harmonic: 3537 Sorted by residual: dihedral pdb=" CA SER E 98 " pdb=" C SER E 98 " pdb=" N HIS E 99 " pdb=" CA HIS E 99 " ideal model delta harmonic sigma weight residual -180.00 -152.30 -27.70 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ASN E 97 " pdb=" C ASN E 97 " pdb=" N SER E 98 " pdb=" CA SER E 98 " ideal model delta harmonic sigma weight residual -180.00 -154.52 -25.48 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA GLU A 124 " pdb=" C GLU A 124 " pdb=" N THR A 125 " pdb=" CA THR A 125 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 5821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 865 0.061 - 0.121: 446 0.121 - 0.181: 181 0.181 - 0.242: 35 0.242 - 0.302: 9 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA ILE B 136 " pdb=" N ILE B 136 " pdb=" C ILE B 136 " pdb=" CB ILE B 136 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA PRO A 128 " pdb=" N PRO A 128 " pdb=" C PRO A 128 " pdb=" CB PRO A 128 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLN B 67 " pdb=" N GLN B 67 " pdb=" C GLN B 67 " pdb=" CB GLN B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1533 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 66 " -0.076 2.00e-02 2.50e+03 4.06e-02 3.29e+01 pdb=" CG TYR E 66 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR E 66 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 66 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR E 66 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR E 66 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR E 66 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 66 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 26 " -0.064 2.00e-02 2.50e+03 3.95e-02 2.73e+01 pdb=" CG PHE G 26 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE G 26 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE G 26 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE G 26 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE G 26 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE G 26 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.067 2.00e-02 2.50e+03 3.60e-02 2.60e+01 pdb=" CG TYR A 139 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.053 2.00e-02 2.50e+03 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 4021 2.96 - 3.45: 10842 3.45 - 3.93: 15793 3.93 - 4.42: 15947 4.42 - 4.90: 29173 Nonbonded interactions: 75776 Sorted by model distance: nonbonded pdb=" CD1 LEU A 9 " pdb=" CD1 ILE A 176 " model vdw 2.478 3.880 nonbonded pdb=" OD1 ASP E 54 " pdb=" N LYS E 55 " model vdw 2.522 3.120 nonbonded pdb=" O LYS E 55 " pdb=" OG SER E 58 " model vdw 2.578 3.040 nonbonded pdb=" OG1 THR B 77 " pdb=" OE1 GLU B 119 " model vdw 2.591 3.040 nonbonded pdb=" OG1 THR A 145 " pdb=" OG1 THR A 178 " model vdw 2.594 3.040 ... (remaining 75771 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 'A' and resid 8 through 223) selection = (chain 'B' and resid 8 through 223) selection = (chain 'C' and resid 8 through 223) selection = chain 'D' selection = (chain 'E' and resid 8 through 223) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 4 through 33) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.360 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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 : 0.011 0.040 9763 Z= 0.701 Angle : 1.616 6.618 13203 Z= 1.128 Chirality : 0.081 0.302 1536 Planarity : 0.014 0.127 1664 Dihedral : 13.350 88.814 3524 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.40 % Allowed : 6.34 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.22), residues: 1203 helix: 0.23 (0.14), residues: 1056 sheet: None (None), residues: 0 loop : 0.03 (0.54), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 110 TYR 0.076 0.015 TYR E 66 PHE 0.064 0.012 PHE G 26 TRP 0.060 0.013 TRP B 147 HIS 0.015 0.002 HIS A 151 Details of bonding type rmsd/Z covalent geometry : bond 0.01144 / 0.70 ( 9763) covalent geometry : angle 1.61618 / 1.13 (13203) hydrogen bonds : bond 0.17374 / 11.43 ( 860) hydrogen bonds : angle 6.72367 / 4.89 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 373 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.9049 (tt0) cc_final: 0.8742 (tm-30) REVERT: B 66 TYR cc_start: 0.9008 (t80) cc_final: 0.8690 (t80) REVERT: B 67 GLN cc_start: 0.9123 (pt0) cc_final: 0.8775 (pp30) REVERT: B 80 GLU cc_start: 0.8683 (tt0) cc_final: 0.8011 (tp30) REVERT: B 102 GLU cc_start: 0.8508 (mp0) cc_final: 0.8223 (pm20) REVERT: B 106 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 166 MET cc_start: 0.9284 (mtp) cc_final: 0.9035 (mtp) REVERT: B 222 PHE cc_start: 0.8711 (m-80) cc_final: 0.8468 (m-10) REVERT: C 21 MET cc_start: 0.8952 (mmm) cc_final: 0.8689 (mpp) REVERT: C 67 GLN cc_start: 0.9334 (pt0) cc_final: 0.9131 (pt0) REVERT: C 68 GLU cc_start: 0.9163 (tt0) cc_final: 0.8854 (tt0) REVERT: C 88 LYS cc_start: 0.8783 (tttm) cc_final: 0.8463 (ttmm) REVERT: C 118 ARG cc_start: 0.8636 (ttm170) cc_final: 0.8398 (ttm110) REVERT: C 161 GLN cc_start: 0.8534 (tp40) cc_final: 0.8280 (pp30) REVERT: C 204 LEU cc_start: 0.8980 (tt) cc_final: 0.8694 (tm) REVERT: C 207 ASP cc_start: 0.9000 (t0) cc_final: 0.8689 (t0) REVERT: D 47 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.8151 (mtp180) REVERT: D 53 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8269 (mm-30) REVERT: D 70 GLN cc_start: 0.9120 (mm110) cc_final: 0.8579 (mm-40) REVERT: D 122 ASN cc_start: 0.9198 (t0) cc_final: 0.8968 (t0) REVERT: D 173 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8569 (mt-10) REVERT: D 208 ASN cc_start: 0.8688 (t0) cc_final: 0.8334 (t0) REVERT: D 220 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7464 (tp-100) REVERT: E 8 ASP cc_start: 0.8393 (p0) cc_final: 0.7896 (p0) REVERT: E 18 LYS cc_start: 0.8500 (mttp) cc_final: 0.8287 (mttp) REVERT: E 37 GLN cc_start: 0.8852 (tt0) cc_final: 0.8638 (tt0) REVERT: E 61 GLU cc_start: 0.9244 (mp0) cc_final: 0.8994 (mp0) REVERT: E 66 TYR cc_start: 0.8767 (t80) cc_final: 0.7836 (t80) REVERT: E 68 GLU cc_start: 0.9328 (tm-30) cc_final: 0.8949 (tm-30) REVERT: E 81 GLN cc_start: 0.8610 (tp40) cc_final: 0.8285 (tp-100) REVERT: E 88 LYS cc_start: 0.8961 (ttmm) cc_final: 0.8574 (ttmm) REVERT: E 89 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7976 (tp30) REVERT: E 94 HIS cc_start: 0.7966 (t70) cc_final: 0.7755 (t-90) REVERT: E 110 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8284 (ttp80) REVERT: E 207 ASP cc_start: 0.8970 (t70) cc_final: 0.8565 (t0) REVERT: E 211 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8892 (mm-30) REVERT: E 220 GLN cc_start: 0.7245 (tm-30) cc_final: 0.7026 (tm-30) REVERT: G 8 ASN cc_start: 0.8233 (m-40) cc_final: 0.7773 (m110) REVERT: G 12 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8540 (mppt) outliers start: 4 outliers final: 2 residues processed: 374 average time/residue: 0.7290 time to fit residues: 287.5399 Evaluate side-chains 260 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 258 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain Z residue 23 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 GLN C 70 GLN C 99 HIS C 197 GLN D 37 GLN D 94 HIS D 99 HIS D 197 GLN E 205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.073305 restraints weight = 16413.055| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.08 r_work: 0.2869 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9763 Z= 0.177 Angle : 0.651 8.245 13203 Z= 0.342 Chirality : 0.041 0.175 1536 Planarity : 0.005 0.042 1664 Dihedral : 4.186 25.647 1310 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 4.02 % Allowed : 18.71 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.01 (0.23), residues: 1203 helix: 2.22 (0.15), residues: 1069 sheet: None (None), residues: 0 loop : 0.20 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 47 TYR 0.026 0.002 TYR A 66 PHE 0.017 0.002 PHE G 26 TRP 0.009 0.001 TRP D 147 HIS 0.007 0.001 HIS D 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 ( 9763) covalent geometry : angle 0.65098 / 0.34 (13203) hydrogen bonds : bond 0.05786 / 3.86 ( 860) hydrogen bonds : angle 4.06015 / 2.94 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7096 (pmt) REVERT: A 53 GLU cc_start: 0.9136 (tt0) cc_final: 0.8779 (tm-30) REVERT: A 70 GLN cc_start: 0.9171 (mt0) cc_final: 0.8878 (mp10) REVERT: A 88 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8661 (tppt) REVERT: A 210 MET cc_start: 0.8923 (ttm) cc_final: 0.8624 (mtp) REVERT: B 66 TYR cc_start: 0.8792 (t80) cc_final: 0.8592 (t80) REVERT: B 67 GLN cc_start: 0.9326 (pt0) cc_final: 0.8855 (pp30) REVERT: B 166 MET cc_start: 0.9273 (mtp) cc_final: 0.8977 (mtp) REVERT: B 203 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 222 PHE cc_start: 0.8692 (m-80) cc_final: 0.8416 (m-10) REVERT: C 21 MET cc_start: 0.8716 (mmm) cc_final: 0.8502 (mpp) REVERT: C 64 ARG cc_start: 0.9043 (ttm110) cc_final: 0.8474 (tpp80) REVERT: C 67 GLN cc_start: 0.9244 (pt0) cc_final: 0.9005 (pt0) REVERT: C 88 LYS cc_start: 0.8674 (tttm) cc_final: 0.8435 (ttmm) REVERT: C 102 GLU cc_start: 0.8407 (pm20) cc_final: 0.7926 (pm20) REVERT: C 159 VAL cc_start: 0.8042 (t) cc_final: 0.7813 (p) REVERT: C 207 ASP cc_start: 0.8864 (t0) cc_final: 0.8502 (t0) REVERT: D 53 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8344 (mm-30) REVERT: D 70 GLN cc_start: 0.8993 (mm110) cc_final: 0.8630 (mm-40) REVERT: D 74 ASP cc_start: 0.6799 (p0) cc_final: 0.6409 (p0) REVERT: D 165 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8381 (mp10) REVERT: D 173 GLU cc_start: 0.8648 (mt-10) cc_final: 0.7673 (tp30) REVERT: D 208 ASN cc_start: 0.8204 (t0) cc_final: 0.7845 (t0) REVERT: D 220 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7296 (tp-100) REVERT: E 66 TYR cc_start: 0.8750 (t80) cc_final: 0.7907 (t80) REVERT: E 84 TYR cc_start: 0.8406 (t80) cc_final: 0.8003 (t80) REVERT: E 166 MET cc_start: 0.9306 (mmm) cc_final: 0.8867 (mpp) REVERT: E 207 ASP cc_start: 0.8896 (t70) cc_final: 0.8441 (t0) REVERT: E 211 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8712 (mm-30) REVERT: G 12 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8024 (mppt) outliers start: 40 outliers final: 11 residues processed: 288 average time/residue: 0.6112 time to fit residues: 187.5914 Evaluate side-chains 249 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 31 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.1407 > 50:) chunk 108 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 GLN B 126 HIS B 197 GLN C 70 GLN C 99 HIS C 197 GLN D 37 GLN D 75 ASN D 94 HIS D 99 HIS D 197 GLN E 5 ASN E 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.102273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073687 restraints weight = 16318.807| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.05 r_work: 0.2884 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9763 Z= 0.155 Angle : 0.609 8.751 13203 Z= 0.314 Chirality : 0.039 0.215 1536 Planarity : 0.004 0.041 1664 Dihedral : 3.926 24.821 1308 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.43 % Allowed : 21.03 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.60 (0.24), residues: 1203 helix: 2.63 (0.15), residues: 1074 sheet: None (None), residues: 0 loop : 0.03 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 118 TYR 0.015 0.001 TYR A 66 PHE 0.028 0.002 PHE C 10 TRP 0.008 0.001 TRP D 57 HIS 0.007 0.001 HIS E 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9763) covalent geometry : angle 0.60882 / 0.31 (13203) hydrogen bonds : bond 0.05154 / 3.46 ( 860) hydrogen bonds : angle 3.81699 / 2.76 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.9120 (tt0) cc_final: 0.8747 (tm-30) REVERT: A 70 GLN cc_start: 0.9212 (mt0) cc_final: 0.8879 (mp10) REVERT: B 53 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8171 (mm-30) REVERT: B 66 TYR cc_start: 0.8847 (t80) cc_final: 0.8625 (t80) REVERT: B 106 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8255 (mt-10) REVERT: B 166 MET cc_start: 0.9278 (mtp) cc_final: 0.9009 (mtp) REVERT: B 203 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8508 (tm-30) REVERT: C 21 MET cc_start: 0.8687 (mmm) cc_final: 0.8442 (mpp) REVERT: C 64 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8544 (tpp80) REVERT: C 67 GLN cc_start: 0.9156 (pt0) cc_final: 0.8935 (pt0) REVERT: C 88 LYS cc_start: 0.8676 (tttm) cc_final: 0.8390 (ttmm) REVERT: C 160 LYS cc_start: 0.9040 (pptt) cc_final: 0.8562 (pptt) REVERT: C 161 GLN cc_start: 0.9107 (tp40) cc_final: 0.8577 (pp30) REVERT: C 207 ASP cc_start: 0.8803 (t0) cc_final: 0.8497 (t0) REVERT: D 53 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8334 (mm-30) REVERT: D 70 GLN cc_start: 0.8950 (mm110) cc_final: 0.8533 (mm-40) REVERT: D 72 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7721 (mmmt) REVERT: D 165 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8441 (mp10) REVERT: D 173 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7683 (tp30) REVERT: D 196 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8008 (m-40) REVERT: D 220 GLN cc_start: 0.7765 (tp-100) cc_final: 0.7430 (tp-100) REVERT: E 8 ASP cc_start: 0.9027 (p0) cc_final: 0.8236 (p0) REVERT: E 66 TYR cc_start: 0.8737 (t80) cc_final: 0.7223 (t80) REVERT: E 84 TYR cc_start: 0.8431 (t80) cc_final: 0.7685 (t80) REVERT: E 88 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8502 (ttmm) REVERT: E 166 MET cc_start: 0.9329 (mmm) cc_final: 0.9022 (mpp) REVERT: E 207 ASP cc_start: 0.8800 (t70) cc_final: 0.8289 (t0) REVERT: E 211 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8624 (mm-30) REVERT: G 12 LYS cc_start: 0.8504 (mtpt) cc_final: 0.7992 (mppt) REVERT: Z 18 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8579 (pp) REVERT: Z 29 LEU cc_start: 0.8635 (tp) cc_final: 0.8327 (mt) outliers start: 44 outliers final: 18 residues processed: 269 average time/residue: 0.6371 time to fit residues: 182.3140 Evaluate side-chains 255 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 28 LEU Chi-restraints excluded: chain Z residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN B 197 GLN B 218 HIS ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 HIS D 197 GLN E 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.071702 restraints weight = 16842.406| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.09 r_work: 0.2844 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9763 Z= 0.190 Angle : 0.612 7.927 13203 Z= 0.314 Chirality : 0.040 0.236 1536 Planarity : 0.004 0.032 1664 Dihedral : 3.788 22.959 1308 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.53 % Allowed : 21.23 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.75 (0.24), residues: 1203 helix: 2.71 (0.15), residues: 1077 sheet: None (None), residues: 0 loop : 0.26 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 47 TYR 0.011 0.001 TYR B 139 PHE 0.018 0.002 PHE G 26 TRP 0.008 0.001 TRP E 32 HIS 0.007 0.001 HIS D 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 9763) covalent geometry : angle 0.61211 / 0.31 (13203) hydrogen bonds : bond 0.04962 / 3.33 ( 860) hydrogen bonds : angle 3.76708 / 2.72 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6914 (pmt) REVERT: A 12 LYS cc_start: 0.9305 (ttpp) cc_final: 0.9100 (ttpp) REVERT: A 53 GLU cc_start: 0.9108 (tt0) cc_final: 0.8738 (tm-30) REVERT: B 66 TYR cc_start: 0.8887 (t80) cc_final: 0.8650 (t80) REVERT: B 67 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8648 (pp30) REVERT: B 106 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8282 (mt-10) REVERT: B 112 MET cc_start: 0.8863 (mtm) cc_final: 0.8566 (mtp) REVERT: B 166 MET cc_start: 0.9291 (mtp) cc_final: 0.8995 (mtp) REVERT: B 203 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8513 (tm-30) REVERT: C 21 MET cc_start: 0.8761 (mmm) cc_final: 0.8538 (mpp) REVERT: C 64 ARG cc_start: 0.8958 (ttm110) cc_final: 0.8645 (tpp80) REVERT: C 67 GLN cc_start: 0.9136 (pt0) cc_final: 0.8912 (pt0) REVERT: C 88 LYS cc_start: 0.8708 (tttm) cc_final: 0.8431 (ttmm) REVERT: C 99 HIS cc_start: 0.7711 (m-70) cc_final: 0.7386 (m-70) REVERT: C 113 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7696 (ttp80) REVERT: C 165 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8476 (tm-30) REVERT: C 166 MET cc_start: 0.9337 (ptp) cc_final: 0.9090 (ptt) REVERT: C 207 ASP cc_start: 0.8815 (t0) cc_final: 0.8507 (t0) REVERT: C 210 MET cc_start: 0.8723 (ttp) cc_final: 0.8488 (ttm) REVERT: D 53 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8346 (mm-30) REVERT: D 70 GLN cc_start: 0.8932 (mm110) cc_final: 0.8449 (mm-40) REVERT: D 72 LYS cc_start: 0.8284 (mmmt) cc_final: 0.7951 (mmmt) REVERT: D 74 ASP cc_start: 0.6940 (p0) cc_final: 0.6623 (p0) REVERT: D 165 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8358 (mp10) REVERT: D 173 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7520 (tp30) REVERT: D 220 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7482 (tp-100) REVERT: E 8 ASP cc_start: 0.8698 (p0) cc_final: 0.8403 (p0) REVERT: E 66 TYR cc_start: 0.8752 (t80) cc_final: 0.7880 (t80) REVERT: E 84 TYR cc_start: 0.8490 (t80) cc_final: 0.8027 (t80) REVERT: E 89 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: E 166 MET cc_start: 0.9378 (mmm) cc_final: 0.9113 (mpp) REVERT: E 207 ASP cc_start: 0.8803 (t70) cc_final: 0.8325 (t0) REVERT: E 211 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8590 (mm-30) REVERT: G 12 LYS cc_start: 0.8494 (mtpt) cc_final: 0.7980 (mppt) outliers start: 55 outliers final: 26 residues processed: 266 average time/residue: 0.6112 time to fit residues: 173.1161 Evaluate side-chains 257 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 12 LYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN B 197 GLN C 70 GLN C 99 HIS D 37 GLN D 99 HIS D 197 GLN E 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.073279 restraints weight = 16638.224| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.06 r_work: 0.2880 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9763 Z= 0.140 Angle : 0.611 8.307 13203 Z= 0.307 Chirality : 0.038 0.263 1536 Planarity : 0.003 0.047 1664 Dihedral : 3.711 21.608 1308 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.23 % Allowed : 22.64 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.94 (0.24), residues: 1203 helix: 2.86 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : 0.11 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 113 TYR 0.012 0.001 TYR A 66 PHE 0.028 0.001 PHE C 10 TRP 0.007 0.001 TRP D 57 HIS 0.007 0.001 HIS D 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9763) covalent geometry : angle 0.61122 / 0.31 (13203) hydrogen bonds : bond 0.04654 / 3.13 ( 860) hydrogen bonds : angle 3.66532 / 2.64 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6792 (pmt) REVERT: A 53 GLU cc_start: 0.9113 (tt0) cc_final: 0.8733 (tm-30) REVERT: B 67 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8764 (pp30) REVERT: B 80 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8392 (tp30) REVERT: B 106 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8339 (mt-10) REVERT: B 166 MET cc_start: 0.9259 (mtp) cc_final: 0.8918 (mtp) REVERT: B 203 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8518 (tm-30) REVERT: C 8 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7245 (p0) REVERT: C 21 MET cc_start: 0.8779 (mmm) cc_final: 0.8520 (mpp) REVERT: C 67 GLN cc_start: 0.9105 (pt0) cc_final: 0.8902 (pt0) REVERT: C 88 LYS cc_start: 0.8675 (tttm) cc_final: 0.8405 (ttmm) REVERT: C 99 HIS cc_start: 0.7825 (m170) cc_final: 0.7555 (m-70) REVERT: C 161 GLN cc_start: 0.9071 (tp40) cc_final: 0.8678 (pp30) REVERT: C 165 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8456 (tm-30) REVERT: C 166 MET cc_start: 0.9301 (ptp) cc_final: 0.9006 (ptt) REVERT: C 207 ASP cc_start: 0.8770 (t0) cc_final: 0.8514 (t0) REVERT: D 53 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8286 (mm-30) REVERT: D 70 GLN cc_start: 0.8906 (mm110) cc_final: 0.8430 (mm-40) REVERT: D 72 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8064 (mmmt) REVERT: D 74 ASP cc_start: 0.6771 (p0) cc_final: 0.6464 (p0) REVERT: D 165 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8421 (mp10) REVERT: D 173 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7657 (tp30) REVERT: D 220 GLN cc_start: 0.7714 (tp-100) cc_final: 0.7454 (tp-100) REVERT: E 66 TYR cc_start: 0.8729 (t80) cc_final: 0.7825 (t80) REVERT: E 84 TYR cc_start: 0.8522 (t80) cc_final: 0.8022 (t80) REVERT: E 89 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: E 166 MET cc_start: 0.9364 (mmm) cc_final: 0.9150 (mpp) REVERT: E 207 ASP cc_start: 0.8777 (t70) cc_final: 0.8269 (t0) REVERT: E 211 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8629 (mm-30) REVERT: F 7 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: G 12 LYS cc_start: 0.8469 (mtpt) cc_final: 0.7928 (mppt) REVERT: Y 15 GLU cc_start: 0.9051 (tp30) cc_final: 0.8762 (tp30) outliers start: 52 outliers final: 24 residues processed: 261 average time/residue: 0.6163 time to fit residues: 171.4462 Evaluate side-chains 257 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN B 197 GLN D 197 GLN E 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.074300 restraints weight = 16751.839| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.04 r_work: 0.2888 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9763 Z= 0.139 Angle : 0.615 10.589 13203 Z= 0.305 Chirality : 0.039 0.365 1536 Planarity : 0.003 0.041 1664 Dihedral : 3.657 20.881 1308 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.43 % Allowed : 23.14 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.05 (0.24), residues: 1203 helix: 2.93 (0.15), residues: 1076 sheet: None (None), residues: 0 loop : 0.11 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 64 TYR 0.016 0.001 TYR B 66 PHE 0.024 0.001 PHE Z 32 TRP 0.006 0.001 TRP D 57 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9763) covalent geometry : angle 0.61549 / 0.31 (13203) hydrogen bonds : bond 0.04501 / 3.03 ( 860) hydrogen bonds : angle 3.63225 / 2.61 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6622 (pmt) REVERT: A 53 GLU cc_start: 0.9099 (tt0) cc_final: 0.8690 (tm-30) REVERT: B 67 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8828 (pp30) REVERT: B 80 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8354 (tp30) REVERT: B 106 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8340 (mt-10) REVERT: B 166 MET cc_start: 0.9269 (mtp) cc_final: 0.8927 (mtp) REVERT: B 203 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 8 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7320 (p0) REVERT: C 21 MET cc_start: 0.8814 (mmm) cc_final: 0.8516 (mpp) REVERT: C 64 ARG cc_start: 0.8913 (ttm110) cc_final: 0.8638 (tpt-90) REVERT: C 67 GLN cc_start: 0.9083 (pt0) cc_final: 0.8841 (pt0) REVERT: C 88 LYS cc_start: 0.8681 (tttm) cc_final: 0.8422 (ttmm) REVERT: C 99 HIS cc_start: 0.7811 (m170) cc_final: 0.7527 (m-70) REVERT: C 161 GLN cc_start: 0.9020 (tp40) cc_final: 0.8689 (pp30) REVERT: C 166 MET cc_start: 0.9305 (ptp) cc_final: 0.9020 (ptt) REVERT: D 53 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8256 (mm-30) REVERT: D 70 GLN cc_start: 0.8884 (mm110) cc_final: 0.8417 (mm-40) REVERT: D 72 LYS cc_start: 0.8456 (mmmt) cc_final: 0.8210 (mmmt) REVERT: D 74 ASP cc_start: 0.6712 (p0) cc_final: 0.6364 (p0) REVERT: D 165 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8388 (mp10) REVERT: D 173 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7385 (tp30) REVERT: D 220 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7500 (tp-100) REVERT: E 66 TYR cc_start: 0.8733 (t80) cc_final: 0.7718 (t80) REVERT: E 84 TYR cc_start: 0.8524 (t80) cc_final: 0.7989 (t80) REVERT: E 89 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: E 166 MET cc_start: 0.9347 (mmm) cc_final: 0.9144 (mpp) REVERT: E 207 ASP cc_start: 0.8759 (t70) cc_final: 0.8237 (t0) REVERT: E 211 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8602 (mm-30) REVERT: F 7 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: G 12 LYS cc_start: 0.8451 (mtpt) cc_final: 0.7931 (mppt) REVERT: Z 32 PHE cc_start: 0.8727 (m-80) cc_final: 0.8457 (m-80) outliers start: 54 outliers final: 20 residues processed: 253 average time/residue: 0.6244 time to fit residues: 168.2009 Evaluate side-chains 249 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 GLN B 197 GLN D 37 GLN D 197 GLN E 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.099824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.072011 restraints weight = 17337.062| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.01 r_work: 0.2882 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9763 Z= 0.148 Angle : 0.644 14.645 13203 Z= 0.317 Chirality : 0.040 0.487 1536 Planarity : 0.004 0.050 1664 Dihedral : 3.584 19.251 1306 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 5.23 % Allowed : 23.84 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.11 (0.24), residues: 1203 helix: 2.96 (0.15), residues: 1078 sheet: None (None), residues: 0 loop : 0.20 (0.59), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 64 TYR 0.027 0.001 TYR B 66 PHE 0.029 0.001 PHE Z 32 TRP 0.006 0.001 TRP D 57 HIS 0.004 0.000 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 9763) covalent geometry : angle 0.64437 / 0.32 (13203) hydrogen bonds : bond 0.04452 / 3.00 ( 860) hydrogen bonds : angle 3.63914 / 2.62 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.9113 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 88 LYS cc_start: 0.9048 (tppt) cc_final: 0.8840 (ttpp) REVERT: B 67 GLN cc_start: 0.9223 (pt0) cc_final: 0.8796 (pp30) REVERT: B 106 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8402 (mt-10) REVERT: B 112 MET cc_start: 0.8777 (mtm) cc_final: 0.8564 (mtp) REVERT: B 166 MET cc_start: 0.9269 (mtp) cc_final: 0.8946 (mtp) REVERT: B 203 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8566 (tm-30) REVERT: C 8 ASP cc_start: 0.8005 (m-30) cc_final: 0.7401 (p0) REVERT: C 21 MET cc_start: 0.8854 (mmm) cc_final: 0.8566 (mpp) REVERT: C 64 ARG cc_start: 0.8921 (ttm110) cc_final: 0.8684 (tpt-90) REVERT: C 67 GLN cc_start: 0.9061 (pt0) cc_final: 0.8804 (pt0) REVERT: C 88 LYS cc_start: 0.8692 (tttm) cc_final: 0.8429 (ttmm) REVERT: C 99 HIS cc_start: 0.7819 (m170) cc_final: 0.7522 (m-70) REVERT: C 161 GLN cc_start: 0.9017 (tp40) cc_final: 0.8734 (pp30) REVERT: C 165 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8315 (tm-30) REVERT: C 166 MET cc_start: 0.9288 (ptp) cc_final: 0.9006 (ptt) REVERT: D 53 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8361 (mm-30) REVERT: D 70 GLN cc_start: 0.8891 (mm110) cc_final: 0.8421 (mm110) REVERT: D 72 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8254 (mmmt) REVERT: D 74 ASP cc_start: 0.6659 (p0) cc_final: 0.6332 (p0) REVERT: D 165 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8325 (mp10) REVERT: D 220 GLN cc_start: 0.7721 (tp-100) cc_final: 0.7494 (tp-100) REVERT: E 12 LYS cc_start: 0.9254 (mppt) cc_final: 0.9037 (pmtt) REVERT: E 66 TYR cc_start: 0.8759 (t80) cc_final: 0.7781 (t80) REVERT: E 84 TYR cc_start: 0.8563 (t80) cc_final: 0.8028 (t80) REVERT: E 99 HIS cc_start: 0.6299 (OUTLIER) cc_final: 0.5701 (t70) REVERT: E 207 ASP cc_start: 0.8777 (t0) cc_final: 0.8296 (t0) REVERT: E 211 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8577 (mm-30) REVERT: F 7 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: G 12 LYS cc_start: 0.8407 (mtpt) cc_final: 0.7903 (mppt) outliers start: 52 outliers final: 23 residues processed: 255 average time/residue: 0.6097 time to fit residues: 165.8191 Evaluate side-chains 251 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 226 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 GLN E 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.102380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.074623 restraints weight = 16669.450| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.00 r_work: 0.2899 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9763 Z= 0.137 Angle : 0.651 15.452 13203 Z= 0.317 Chirality : 0.040 0.437 1536 Planarity : 0.003 0.039 1664 Dihedral : 3.596 18.908 1306 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.02 % Allowed : 26.66 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.13 (0.24), residues: 1203 helix: 2.99 (0.15), residues: 1075 sheet: None (None), residues: 0 loop : 0.12 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 64 TYR 0.029 0.001 TYR B 66 PHE 0.016 0.001 PHE Z 32 TRP 0.006 0.001 TRP D 57 HIS 0.004 0.000 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9763) covalent geometry : angle 0.65064 / 0.32 (13203) hydrogen bonds : bond 0.04351 / 2.94 ( 860) hydrogen bonds : angle 3.62381 / 2.61 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.9104 (tt0) cc_final: 0.8723 (tm-30) REVERT: B 50 GLU cc_start: 0.9013 (tt0) cc_final: 0.8674 (tp30) REVERT: B 67 GLN cc_start: 0.9200 (pt0) cc_final: 0.8736 (pp30) REVERT: B 106 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8394 (mt-10) REVERT: B 112 MET cc_start: 0.8770 (mtm) cc_final: 0.8528 (mtp) REVERT: B 166 MET cc_start: 0.9244 (mtp) cc_final: 0.8928 (mtp) REVERT: B 203 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8569 (tm-30) REVERT: C 21 MET cc_start: 0.8828 (mmm) cc_final: 0.8542 (mpp) REVERT: C 88 LYS cc_start: 0.8672 (tttm) cc_final: 0.8434 (ttmm) REVERT: C 99 HIS cc_start: 0.7834 (m170) cc_final: 0.7354 (m-70) REVERT: C 161 GLN cc_start: 0.8977 (tp40) cc_final: 0.8665 (pp30) REVERT: C 165 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 166 MET cc_start: 0.9277 (ptp) cc_final: 0.8981 (ptt) REVERT: C 212 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8385 (mt-10) REVERT: D 53 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8322 (mm-30) REVERT: D 70 GLN cc_start: 0.8868 (mm110) cc_final: 0.8403 (mm110) REVERT: D 72 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8272 (mmmt) REVERT: D 74 ASP cc_start: 0.6558 (p0) cc_final: 0.6232 (p0) REVERT: D 165 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8184 (mp10) REVERT: D 196 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8199 (m-40) REVERT: D 220 GLN cc_start: 0.7726 (tp-100) cc_final: 0.7498 (tp-100) REVERT: E 8 ASP cc_start: 0.8915 (p0) cc_final: 0.8631 (p0) REVERT: E 12 LYS cc_start: 0.9229 (mppt) cc_final: 0.8996 (pmtt) REVERT: E 66 TYR cc_start: 0.8755 (t80) cc_final: 0.8014 (t80) REVERT: E 99 HIS cc_start: 0.6343 (OUTLIER) cc_final: 0.5725 (t70) REVERT: E 203 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8484 (tm-30) REVERT: E 207 ASP cc_start: 0.8787 (t0) cc_final: 0.8239 (t0) REVERT: E 211 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8539 (mm-30) REVERT: G 12 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7856 (mppt) outliers start: 30 outliers final: 17 residues processed: 246 average time/residue: 0.6274 time to fit residues: 164.2078 Evaluate side-chains 245 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 67 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 GLN C 75 ASN D 37 GLN D 197 GLN E 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.103134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.074973 restraints weight = 16474.307| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.03 r_work: 0.2919 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9763 Z= 0.138 Angle : 0.683 14.268 13203 Z= 0.329 Chirality : 0.040 0.428 1536 Planarity : 0.004 0.057 1664 Dihedral : 3.604 17.702 1306 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.72 % Allowed : 25.96 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.13 (0.24), residues: 1203 helix: 3.01 (0.15), residues: 1074 sheet: None (None), residues: 0 loop : -0.08 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 64 TYR 0.026 0.001 TYR B 66 PHE 0.019 0.001 PHE Z 32 TRP 0.006 0.001 TRP D 57 HIS 0.004 0.000 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9763) covalent geometry : angle 0.68276 / 0.33 (13203) hydrogen bonds : bond 0.04248 / 2.87 ( 860) hydrogen bonds : angle 3.62342 / 2.60 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.9099 (tt0) cc_final: 0.8725 (tm-30) REVERT: A 81 GLN cc_start: 0.7842 (tp-100) cc_final: 0.7536 (tm-30) REVERT: A 88 LYS cc_start: 0.9161 (ttpp) cc_final: 0.8829 (ttmt) REVERT: B 50 GLU cc_start: 0.9019 (tt0) cc_final: 0.8676 (tp30) REVERT: B 53 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8146 (mp0) REVERT: B 67 GLN cc_start: 0.9158 (pt0) cc_final: 0.8685 (pp30) REVERT: B 80 GLU cc_start: 0.8787 (tt0) cc_final: 0.8284 (tp30) REVERT: B 102 GLU cc_start: 0.8498 (mp0) cc_final: 0.8232 (pm20) REVERT: B 106 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8403 (mt-10) REVERT: B 112 MET cc_start: 0.8752 (mtm) cc_final: 0.8543 (mtp) REVERT: B 166 MET cc_start: 0.9223 (mtp) cc_final: 0.9002 (mtp) REVERT: B 203 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8503 (tm-30) REVERT: B 211 GLU cc_start: 0.8631 (tt0) cc_final: 0.8289 (tm-30) REVERT: C 21 MET cc_start: 0.8795 (mmm) cc_final: 0.8555 (mpp) REVERT: C 88 LYS cc_start: 0.8667 (tttm) cc_final: 0.8434 (ttmm) REVERT: C 99 HIS cc_start: 0.7736 (m170) cc_final: 0.7396 (m-70) REVERT: C 161 GLN cc_start: 0.8966 (tp40) cc_final: 0.8683 (pp30) REVERT: C 166 MET cc_start: 0.9277 (ptp) cc_final: 0.8994 (ptt) REVERT: C 212 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8415 (mt-10) REVERT: D 53 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8312 (mm-30) REVERT: D 70 GLN cc_start: 0.8882 (mm110) cc_final: 0.8432 (mm110) REVERT: D 72 LYS cc_start: 0.8474 (mmmt) cc_final: 0.8205 (mmmt) REVERT: D 165 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8054 (mp10) REVERT: D 196 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8214 (m-40) REVERT: D 220 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7524 (tp-100) REVERT: E 66 TYR cc_start: 0.8797 (t80) cc_final: 0.8120 (t80) REVERT: E 99 HIS cc_start: 0.6392 (OUTLIER) cc_final: 0.5808 (t70) REVERT: E 203 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8491 (tm-30) REVERT: E 207 ASP cc_start: 0.8793 (t0) cc_final: 0.8242 (t0) REVERT: E 211 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8531 (mm-30) REVERT: F 7 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: G 6 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8627 (pm20) REVERT: G 12 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7850 (mppt) outliers start: 37 outliers final: 20 residues processed: 259 average time/residue: 0.6299 time to fit residues: 173.6039 Evaluate side-chains 259 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 GLN D 197 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.074212 restraints weight = 16586.741| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.03 r_work: 0.2903 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9763 Z= 0.152 Angle : 0.686 13.495 13203 Z= 0.335 Chirality : 0.040 0.418 1536 Planarity : 0.004 0.059 1664 Dihedral : 3.593 17.376 1306 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.82 % Allowed : 27.26 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.12 (0.24), residues: 1203 helix: 3.03 (0.15), residues: 1073 sheet: None (None), residues: 0 loop : -0.29 (0.57), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 64 TYR 0.027 0.001 TYR B 66 PHE 0.018 0.001 PHE Z 32 TRP 0.006 0.001 TRP B 147 HIS 0.004 0.000 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9763) covalent geometry : angle 0.68566 / 0.33 (13203) hydrogen bonds : bond 0.04302 / 2.90 ( 860) hydrogen bonds : angle 3.66150 / 2.63 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 229 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.9106 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 88 LYS cc_start: 0.9168 (ttpp) cc_final: 0.8838 (ttmt) REVERT: A 166 MET cc_start: 0.9077 (ptp) cc_final: 0.8863 (pmm) REVERT: B 50 GLU cc_start: 0.9015 (tt0) cc_final: 0.8717 (tp30) REVERT: B 53 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8145 (mp0) REVERT: B 67 GLN cc_start: 0.9137 (pt0) cc_final: 0.8680 (pp30) REVERT: B 106 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8419 (mt-10) REVERT: B 112 MET cc_start: 0.8805 (mtm) cc_final: 0.8570 (mtp) REVERT: B 166 MET cc_start: 0.9223 (mtp) cc_final: 0.9004 (mtp) REVERT: C 21 MET cc_start: 0.8808 (mmm) cc_final: 0.8531 (mpp) REVERT: C 67 GLN cc_start: 0.8939 (pt0) cc_final: 0.8627 (pm20) REVERT: C 88 LYS cc_start: 0.8670 (tttm) cc_final: 0.8443 (ttmm) REVERT: C 99 HIS cc_start: 0.7749 (m170) cc_final: 0.7423 (m-70) REVERT: C 161 GLN cc_start: 0.8962 (tp40) cc_final: 0.8674 (pp30) REVERT: C 165 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8315 (tm-30) REVERT: C 166 MET cc_start: 0.9274 (ptp) cc_final: 0.9007 (ptt) REVERT: C 212 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8426 (mt-10) REVERT: D 53 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8303 (mm-30) REVERT: D 70 GLN cc_start: 0.8846 (mm110) cc_final: 0.8393 (mm110) REVERT: D 72 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8212 (mmmt) REVERT: D 165 GLN cc_start: 0.8300 (mm-40) cc_final: 0.8045 (mp10) REVERT: D 196 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8256 (m-40) REVERT: D 220 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7546 (tp-100) REVERT: E 66 TYR cc_start: 0.8762 (t80) cc_final: 0.8053 (t80) REVERT: E 99 HIS cc_start: 0.6509 (OUTLIER) cc_final: 0.5982 (t70) REVERT: E 203 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8464 (tm-30) REVERT: E 207 ASP cc_start: 0.8811 (t0) cc_final: 0.8314 (t0) REVERT: E 211 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8573 (mm-30) REVERT: F 7 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: G 6 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8645 (pm20) REVERT: G 12 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7847 (mppt) outliers start: 28 outliers final: 21 residues processed: 243 average time/residue: 0.5751 time to fit residues: 148.7521 Evaluate side-chains 248 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 10 LYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 197 GLN D 197 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.101363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.073008 restraints weight = 16604.062| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.03 r_work: 0.2879 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9763 Z= 0.177 Angle : 0.707 12.819 13203 Z= 0.346 Chirality : 0.041 0.410 1536 Planarity : 0.004 0.057 1664 Dihedral : 3.569 16.697 1306 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.62 % Allowed : 26.96 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.09 (0.24), residues: 1203 helix: 3.01 (0.15), residues: 1073 sheet: None (None), residues: 0 loop : -0.36 (0.56), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 64 TYR 0.029 0.001 TYR B 66 PHE 0.014 0.001 PHE B 222 TRP 0.006 0.001 TRP E 32 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 9763) covalent geometry : angle 0.70721 / 0.35 (13203) hydrogen bonds : bond 0.04440 / 3.00 ( 860) hydrogen bonds : angle 3.68832 / 2.65 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.10 seconds wall clock time: 63 minutes 43.94 seconds (3823.94 seconds total)