Starting phenix.real_space_refine on Sun Apr 5 11:40:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kq0_62493/04_2026/9kq0_62493.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kq0_62493/04_2026/9kq0_62493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kq0_62493/04_2026/9kq0_62493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kq0_62493/04_2026/9kq0_62493.map" model { file = "/net/cci-nas-00/data/ceres_data/9kq0_62493/04_2026/9kq0_62493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kq0_62493/04_2026/9kq0_62493.cif" } resolution = 3.6 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= 0.001 sd= 0.016 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 6527 2.51 5 N 1709 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10048 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1784 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1738 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain: "C" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1758 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain: "D" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1705 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" 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: "F" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 179 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "G" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 191 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "H" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 214 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 237 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 164 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "K" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 129 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 212 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 2.60, per 1000 atoms: 0.26 Number of scatterers: 10048 At special positions: 0 Unit cell: (84, 94.08, 121.8, 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 1771 8.00 N 1709 7.00 C 6527 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: 0.93 Conformation dependent library (CDL) restraints added in 462.9 milliseconds 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 91.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 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 73 removed outlier: 3.900A pdb=" N LEU A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.721A pdb=" N ILE A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 Processing helix chain 'A' and resid 126 through 158 removed outlier: 4.051A pdb=" N LEU A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Proline residue: A 138 - end of helix removed outlier: 3.785A pdb=" N ALA A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 230 removed outlier: 3.868A pdb=" N ALA A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Proline residue: A 187 - end of helix removed outlier: 4.175A pdb=" N MET A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 12 Processing helix chain 'B' and resid 14 through 57 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 78 through 97 removed outlier: 4.062A pdb=" N HIS B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 124 Processing helix chain 'B' and resid 126 through 158 removed outlier: 3.914A pdb=" N LEU B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 167 through 222 Proline residue: B 187 - end of helix Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 14 through 58 removed outlier: 3.553A pdb=" N ARG C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 97 removed outlier: 3.640A pdb=" N ILE C 82 " --> pdb=" O GLY C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 124 Processing helix chain 'C' and resid 126 through 157 removed outlier: 3.924A pdb=" N LEU C 130 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 163 through 190 removed outlier: 3.993A pdb=" N VAL C 167 " --> pdb=" O THR C 163 " (cutoff:3.500A) Proline residue: C 169 - end of helix removed outlier: 3.880A pdb=" N THR C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 191 through 225 Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 15 through 57 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.519A pdb=" N LEU D 76 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR D 77 " --> pdb=" O ASP D 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 77' Processing helix chain 'D' and resid 78 through 97 removed outlier: 3.636A pdb=" N ILE D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'D' and resid 126 through 159 Proline residue: D 138 - end of helix Processing helix chain 'D' and resid 167 through 220 removed outlier: 3.581A pdb=" N ILE D 171 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Proline residue: D 187 - end of helix removed outlier: 3.674A pdb=" N GLN D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 12 Processing helix chain 'E' and resid 14 through 57 Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'E' and resid 73 through 77 removed outlier: 4.253A pdb=" N LEU E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR E 77 " --> pdb=" O ASP E 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 77' Processing helix chain 'E' and resid 78 through 98 Processing helix chain 'E' and resid 100 through 125 removed outlier: 3.913A pdb=" N VAL E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 removed outlier: 4.327A pdb=" N LEU E 130 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 158 Processing helix chain 'E' and resid 163 through 224 removed outlier: 4.056A pdb=" N VAL E 167 " --> pdb=" O THR E 163 " (cutoff:3.500A) Proline residue: E 169 - end of helix removed outlier: 4.023A pdb=" N ALA E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 173 " --> pdb=" O PRO E 169 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Proline residue: E 187 - end of helix removed outlier: 4.207A pdb=" N ASN E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 33 removed outlier: 4.155A pdb=" N VAL F 24 " --> pdb=" O PRO F 20 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 35 removed outlier: 4.012A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 35 Processing helix chain 'I' and resid 9 through 37 Processing helix chain 'J' and resid 9 through 31 Processing helix chain 'K' and resid 9 through 25 Processing helix chain 'L' and resid 9 through 35 920 hydrogen bonds defined for protein. 2760 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: 1.36 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3249 1.34 - 1.46: 1633 1.46 - 1.57: 5267 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 10231 Sorted by residual: bond pdb=" C ALA C 168 " pdb=" N PRO C 169 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.76e+00 bond pdb=" CA ILE D 186 " pdb=" C ILE D 186 " ideal model delta sigma weight residual 1.523 1.532 -0.009 9.20e-03 1.18e+04 1.04e+00 bond pdb=" CD GLU C 173 " pdb=" OE1 GLU C 173 " ideal model delta sigma weight residual 1.249 1.230 0.019 1.90e-02 2.77e+03 1.03e+00 bond pdb=" C ILE D 186 " pdb=" O ILE D 186 " ideal model delta sigma weight residual 1.242 1.250 -0.008 8.60e-03 1.35e+04 8.90e-01 bond pdb=" CG GLU C 173 " pdb=" CD GLU C 173 " ideal model delta sigma weight residual 1.516 1.493 0.023 2.50e-02 1.60e+03 8.52e-01 ... (remaining 10226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 13679 1.68 - 3.36: 120 3.36 - 5.03: 33 5.03 - 6.71: 11 6.71 - 8.39: 1 Bond angle restraints: 13844 Sorted by residual: angle pdb=" N GLU C 173 " pdb=" CA GLU C 173 " pdb=" CB GLU C 173 " ideal model delta sigma weight residual 110.39 116.43 -6.04 1.66e+00 3.63e-01 1.32e+01 angle pdb=" C GLN D 220 " pdb=" N ALA D 221 " pdb=" CA ALA D 221 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C ILE D 186 " pdb=" CA ILE D 186 " pdb=" CB ILE D 186 " ideal model delta sigma weight residual 114.00 109.86 4.14 1.31e+00 5.83e-01 9.99e+00 angle pdb=" C ALA C 172 " pdb=" N GLU C 173 " pdb=" CA GLU C 173 " ideal model delta sigma weight residual 120.72 115.84 4.88 1.67e+00 3.59e-01 8.53e+00 angle pdb=" N GLU D 173 " pdb=" CA GLU D 173 " pdb=" CB GLU D 173 " ideal model delta sigma weight residual 110.28 114.63 -4.35 1.55e+00 4.16e-01 7.87e+00 ... (remaining 13839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5359 17.63 - 35.27: 623 35.27 - 52.90: 93 52.90 - 70.53: 12 70.53 - 88.16: 11 Dihedral angle restraints: 6098 sinusoidal: 2360 harmonic: 3738 Sorted by residual: dihedral pdb=" CG ARG E 194 " pdb=" CD ARG E 194 " pdb=" NE ARG E 194 " pdb=" CZ ARG E 194 " ideal model delta sinusoidal sigma weight residual -90.00 -134.97 44.97 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CB GLU C 89 " pdb=" CG GLU C 89 " pdb=" CD GLU C 89 " pdb=" OE1 GLU C 89 " ideal model delta sinusoidal sigma weight residual 0.00 83.58 -83.58 1 3.00e+01 1.11e-03 9.47e+00 dihedral pdb=" CB LYS D 160 " pdb=" CG LYS D 160 " pdb=" CD LYS D 160 " pdb=" CE LYS D 160 " ideal model delta sinusoidal sigma weight residual 60.00 116.16 -56.16 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 6095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1120 0.029 - 0.058: 308 0.058 - 0.087: 162 0.087 - 0.116: 41 0.116 - 0.145: 2 Chirality restraints: 1633 Sorted by residual: chirality pdb=" CA GLU C 173 " pdb=" N GLU C 173 " pdb=" C GLU C 173 " pdb=" CB GLU C 173 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE C 60 " pdb=" N ILE C 60 " pdb=" C ILE C 60 " pdb=" CB ILE C 60 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA PRO E 128 " pdb=" N PRO E 128 " pdb=" C PRO E 128 " pdb=" CB PRO E 128 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.17e-01 ... (remaining 1630 not shown) Planarity restraints: 1736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 84 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C TYR B 84 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR B 84 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 85 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 85 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C SER B 85 " 0.026 2.00e-02 2.50e+03 pdb=" O SER B 85 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY B 86 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 89 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C GLU B 89 " 0.025 2.00e-02 2.50e+03 pdb=" O GLU B 89 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE B 90 " -0.008 2.00e-02 2.50e+03 ... (remaining 1733 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 866 2.74 - 3.28: 10801 3.28 - 3.82: 17955 3.82 - 4.36: 17483 4.36 - 4.90: 32043 Nonbonded interactions: 79148 Sorted by model distance: nonbonded pdb=" OG1 THR D 145 " pdb=" OG1 THR D 178 " model vdw 2.201 3.040 nonbonded pdb=" OE1 GLN E 81 " pdb=" OG SER E 115 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLN C 81 " pdb=" OG SER C 85 " model vdw 2.239 3.040 nonbonded pdb=" OE1 GLU E 61 " pdb=" OG SER E 63 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG D 38 " pdb=" O LEU D 123 " model vdw 2.287 3.120 ... (remaining 79143 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 6 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 93 or (resid 94 through 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 222)) selection = (chain 'B' and (resid 6 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 93 or (resid 94 through 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 164 or (r \ esid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 t \ hrough 222)) selection = (chain 'C' and (resid 6 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 93 or (resid 94 through 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 164 or (r \ esid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 t \ hrough 222)) selection = (chain 'D' and (resid 6 through 164 or (resid 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 through 222)) selection = (chain 'E' and (resid 6 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 93 or (resid 94 through 96 and (nam \ e N or name CA or name C or name O or name CB )) or resid 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 164 or (r \ esid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 t \ hrough 222)) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 13 through 35) } ncs_group { reference = (chain 'H' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 or (resid 10 through 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 or (resid 13 through 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 26 or (resid 27 through 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 31)) selection = (chain 'I' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 or (resid 10 through 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 or (resid 13 through 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 26 or (resid 27 through 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 31)) selection = (chain 'J' and (resid 8 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 31)) selection = (chain 'L' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 or (resid 10 through 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 or (resid 13 through 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 26 or (resid 27 through 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 31)) } 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 group one per residue 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.002 0.028 10231 Z= 0.119 Angle : 0.482 8.391 13844 Z= 0.258 Chirality : 0.035 0.145 1633 Planarity : 0.003 0.031 1736 Dihedral : 14.865 88.164 3662 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 4.46 (0.24), residues: 1265 helix: 3.42 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -1.65 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.007 0.001 TYR B 192 PHE 0.014 0.001 PHE A 222 TRP 0.007 0.001 TRP C 147 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00232 (10231) covalent geometry : angle 0.48243 (13844) hydrogen bonds : bond 0.10720 ( 920) hydrogen bonds : angle 4.18409 ( 2760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7592 (m) cc_final: 0.7316 (m) REVERT: A 154 ILE cc_start: 0.9241 (pt) cc_final: 0.8963 (mm) REVERT: A 203 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 218 HIS cc_start: 0.8641 (t70) cc_final: 0.8346 (t70) REVERT: B 207 ASP cc_start: 0.8533 (t0) cc_final: 0.7671 (t0) REVERT: C 84 TYR cc_start: 0.7728 (t80) cc_final: 0.7363 (t80) REVERT: C 176 ILE cc_start: 0.8986 (mm) cc_final: 0.8655 (mt) REVERT: C 203 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7702 (tm-30) REVERT: C 217 LEU cc_start: 0.9019 (mt) cc_final: 0.8547 (tt) REVERT: D 12 LYS cc_start: 0.8898 (tptt) cc_final: 0.8550 (tptt) REVERT: D 53 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 87 PHE cc_start: 0.8224 (t80) cc_final: 0.7515 (t80) REVERT: D 120 LEU cc_start: 0.7628 (mt) cc_final: 0.7271 (mm) REVERT: D 150 MET cc_start: 0.8107 (tmm) cc_final: 0.7868 (tmm) REVERT: D 210 MET cc_start: 0.8341 (ttp) cc_final: 0.8031 (ttp) REVERT: E 7 LEU cc_start: 0.8791 (mt) cc_final: 0.8588 (pp) REVERT: E 84 TYR cc_start: 0.7399 (t80) cc_final: 0.7007 (t80) REVERT: E 118 ARG cc_start: 0.7726 (tpt-90) cc_final: 0.7296 (mtp-110) REVERT: E 150 MET cc_start: 0.8605 (tmm) cc_final: 0.8183 (tmm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.1063 time to fit residues: 48.6794 Evaluate side-chains 233 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN E 5 ASN E 208 ASN K 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.149977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.115588 restraints weight = 22882.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.119369 restraints weight = 12060.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.121719 restraints weight = 8533.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.122945 restraints weight = 7168.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.123372 restraints weight = 6586.549| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10231 Z= 0.192 Angle : 0.657 10.200 13844 Z= 0.338 Chirality : 0.040 0.174 1633 Planarity : 0.004 0.037 1736 Dihedral : 3.410 16.929 1368 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 3.08 % Allowed : 14.05 % Favored : 82.87 % 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: 3.88 (0.23), residues: 1265 helix: 3.00 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -2.06 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 110 TYR 0.020 0.002 TYR E 66 PHE 0.022 0.002 PHE E 209 TRP 0.014 0.001 TRP D 57 HIS 0.003 0.001 HIS D 126 Details of bonding type rmsd covalent geometry : bond 0.00429 (10231) covalent geometry : angle 0.65708 (13844) hydrogen bonds : bond 0.05062 ( 920) hydrogen bonds : angle 3.70249 ( 2760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8270 (mtm) cc_final: 0.7931 (mtm) REVERT: A 39 THR cc_start: 0.7642 (m) cc_final: 0.7354 (m) REVERT: A 88 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8777 (mtmt) REVERT: A 154 ILE cc_start: 0.9294 (pt) cc_final: 0.9029 (mm) REVERT: A 203 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 218 HIS cc_start: 0.8620 (t70) cc_final: 0.8266 (t70) REVERT: B 12 LYS cc_start: 0.8955 (pttp) cc_final: 0.8450 (pttm) REVERT: B 206 TYR cc_start: 0.8728 (m-10) cc_final: 0.8480 (m-10) REVERT: B 207 ASP cc_start: 0.8605 (t0) cc_final: 0.8298 (t0) REVERT: C 84 TYR cc_start: 0.7835 (t80) cc_final: 0.7332 (t80) REVERT: C 203 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8154 (tm-30) REVERT: C 217 LEU cc_start: 0.9108 (mt) cc_final: 0.8665 (tt) REVERT: D 12 LYS cc_start: 0.8784 (tptt) cc_final: 0.8453 (tptt) REVERT: D 203 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: D 210 MET cc_start: 0.8350 (ttp) cc_final: 0.8101 (ttp) REVERT: E 4 MET cc_start: 0.8044 (ppp) cc_final: 0.6937 (ppp) REVERT: E 7 LEU cc_start: 0.8907 (mt) cc_final: 0.8680 (pp) REVERT: E 84 TYR cc_start: 0.7396 (t80) cc_final: 0.6926 (t80) REVERT: E 118 ARG cc_start: 0.7851 (tpt-90) cc_final: 0.7429 (mtp-110) REVERT: E 150 MET cc_start: 0.8678 (tmm) cc_final: 0.8171 (tmm) outliers start: 32 outliers final: 18 residues processed: 262 average time/residue: 0.0960 time to fit residues: 35.0285 Evaluate side-chains 246 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain J residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 109 optimal weight: 0.0030 chunk 7 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 HIS K 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.152906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.120699 restraints weight = 23078.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.123299 restraints weight = 13857.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.124973 restraints weight = 8868.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.125047 restraints weight = 7829.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.125101 restraints weight = 7718.458| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10231 Z= 0.134 Angle : 0.583 9.685 13844 Z= 0.299 Chirality : 0.037 0.192 1633 Planarity : 0.003 0.042 1736 Dihedral : 3.430 16.957 1368 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.31 % Rotamer: Outliers : 2.50 % Allowed : 17.13 % Favored : 80.37 % 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: 3.89 (0.23), residues: 1265 helix: 3.02 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -2.03 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.013 0.001 TYR D 66 PHE 0.024 0.002 PHE A 213 TRP 0.022 0.001 TRP D 57 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00269 (10231) covalent geometry : angle 0.58269 (13844) hydrogen bonds : bond 0.04625 ( 920) hydrogen bonds : angle 3.54673 ( 2760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7674 (m) cc_final: 0.7399 (m) REVERT: A 84 TYR cc_start: 0.8272 (t80) cc_final: 0.7995 (t80) REVERT: A 88 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8663 (mtmt) REVERT: A 154 ILE cc_start: 0.9315 (pt) cc_final: 0.9113 (mm) REVERT: A 203 GLU cc_start: 0.8247 (tm-30) cc_final: 0.8038 (tm-30) REVERT: A 218 HIS cc_start: 0.8705 (t70) cc_final: 0.8379 (t70) REVERT: B 12 LYS cc_start: 0.8968 (pttp) cc_final: 0.8421 (pttm) REVERT: B 207 ASP cc_start: 0.8770 (t0) cc_final: 0.8518 (t0) REVERT: C 84 TYR cc_start: 0.7864 (t80) cc_final: 0.7329 (t80) REVERT: C 203 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 217 LEU cc_start: 0.9092 (mt) cc_final: 0.8657 (tt) REVERT: D 12 LYS cc_start: 0.8833 (tptt) cc_final: 0.8420 (tptt) REVERT: D 35 ILE cc_start: 0.7598 (mt) cc_final: 0.7311 (mt) REVERT: D 120 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7905 (mm) REVERT: D 203 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: E 4 MET cc_start: 0.7926 (ppp) cc_final: 0.6812 (ppp) REVERT: E 7 LEU cc_start: 0.8980 (mt) cc_final: 0.8718 (pp) REVERT: E 81 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7027 (tm-30) REVERT: E 84 TYR cc_start: 0.7174 (t80) cc_final: 0.6929 (t80) REVERT: E 150 MET cc_start: 0.8700 (tmm) cc_final: 0.8180 (tmm) outliers start: 26 outliers final: 14 residues processed: 252 average time/residue: 0.0978 time to fit residues: 34.4525 Evaluate side-chains 233 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN K 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.150508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.116415 restraints weight = 23268.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.120314 restraints weight = 12067.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.122696 restraints weight = 8418.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.123859 restraints weight = 7029.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.124638 restraints weight = 6461.834| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10231 Z= 0.142 Angle : 0.587 8.601 13844 Z= 0.303 Chirality : 0.038 0.168 1633 Planarity : 0.003 0.041 1736 Dihedral : 3.416 17.831 1368 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % Rotamer: Outliers : 3.46 % Allowed : 18.86 % Favored : 77.67 % 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: 3.83 (0.23), residues: 1265 helix: 2.96 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.92 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.024 0.001 TYR E 66 PHE 0.023 0.001 PHE A 213 TRP 0.024 0.001 TRP D 57 HIS 0.007 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00303 (10231) covalent geometry : angle 0.58732 (13844) hydrogen bonds : bond 0.04584 ( 920) hydrogen bonds : angle 3.55971 ( 2760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7631 (m) cc_final: 0.7349 (m) REVERT: A 84 TYR cc_start: 0.8285 (t80) cc_final: 0.7836 (t80) REVERT: A 88 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8715 (mtmt) REVERT: A 110 ARG cc_start: 0.8608 (tmm160) cc_final: 0.8315 (ttp80) REVERT: A 154 ILE cc_start: 0.9260 (pt) cc_final: 0.9027 (mm) REVERT: A 218 HIS cc_start: 0.8683 (t70) cc_final: 0.8259 (t70) REVERT: B 12 LYS cc_start: 0.8889 (pttp) cc_final: 0.8352 (pttm) REVERT: B 112 MET cc_start: 0.8126 (mtt) cc_final: 0.7895 (mtt) REVERT: B 206 TYR cc_start: 0.8762 (m-10) cc_final: 0.8494 (m-10) REVERT: B 207 ASP cc_start: 0.8729 (t0) cc_final: 0.8476 (t0) REVERT: C 84 TYR cc_start: 0.7814 (t80) cc_final: 0.7384 (t80) REVERT: C 203 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8088 (tm-30) REVERT: C 217 LEU cc_start: 0.9083 (mt) cc_final: 0.8644 (tt) REVERT: D 12 LYS cc_start: 0.8659 (tptt) cc_final: 0.8309 (tptt) REVERT: D 57 TRP cc_start: 0.7274 (m-10) cc_final: 0.6119 (m-10) REVERT: D 120 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7985 (mm) REVERT: D 203 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: D 210 MET cc_start: 0.8481 (ttp) cc_final: 0.8203 (ttp) REVERT: E 4 MET cc_start: 0.7909 (ppp) cc_final: 0.6718 (ppp) REVERT: E 7 LEU cc_start: 0.8865 (mt) cc_final: 0.8639 (pp) REVERT: E 150 MET cc_start: 0.8670 (tmm) cc_final: 0.8199 (tmm) outliers start: 36 outliers final: 25 residues processed: 240 average time/residue: 0.0990 time to fit residues: 33.1863 Evaluate side-chains 247 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 218 HIS I 8 GLN K 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.152858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.119455 restraints weight = 23290.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.123486 restraints weight = 11870.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.125783 restraints weight = 8310.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.126685 restraints weight = 6988.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.127683 restraints weight = 6487.346| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10231 Z= 0.134 Angle : 0.594 16.110 13844 Z= 0.301 Chirality : 0.037 0.201 1633 Planarity : 0.003 0.034 1736 Dihedral : 3.422 18.079 1368 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.45 % Favored : 97.47 % Rotamer: Outliers : 2.98 % Allowed : 21.08 % Favored : 75.94 % 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: 3.84 (0.23), residues: 1265 helix: 2.97 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.87 (0.49), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 113 TYR 0.028 0.001 TYR E 66 PHE 0.027 0.001 PHE E 87 TRP 0.016 0.001 TRP D 57 HIS 0.004 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00283 (10231) covalent geometry : angle 0.59406 (13844) hydrogen bonds : bond 0.04513 ( 920) hydrogen bonds : angle 3.52195 ( 2760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7614 (m) cc_final: 0.7335 (m) REVERT: A 72 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6611 (mttm) REVERT: A 84 TYR cc_start: 0.8250 (t80) cc_final: 0.7952 (t80) REVERT: A 88 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8701 (mtmt) REVERT: A 110 ARG cc_start: 0.8553 (tmm160) cc_final: 0.8269 (ttp80) REVERT: A 154 ILE cc_start: 0.9244 (pt) cc_final: 0.9006 (mm) REVERT: A 207 ASP cc_start: 0.8418 (t70) cc_final: 0.8128 (t0) REVERT: A 218 HIS cc_start: 0.8628 (t70) cc_final: 0.8209 (t70) REVERT: B 12 LYS cc_start: 0.8891 (pttp) cc_final: 0.8450 (pttm) REVERT: B 207 ASP cc_start: 0.8682 (t0) cc_final: 0.8446 (t0) REVERT: B 210 MET cc_start: 0.8241 (tpp) cc_final: 0.8016 (ttt) REVERT: C 84 TYR cc_start: 0.7723 (t80) cc_final: 0.7387 (t80) REVERT: C 203 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 217 LEU cc_start: 0.9082 (mt) cc_final: 0.8628 (tt) REVERT: D 12 LYS cc_start: 0.8610 (tptt) cc_final: 0.8269 (tptt) REVERT: D 35 ILE cc_start: 0.7654 (mt) cc_final: 0.7395 (mt) REVERT: D 84 TYR cc_start: 0.6296 (t80) cc_final: 0.6073 (t80) REVERT: D 112 MET cc_start: 0.8263 (tpp) cc_final: 0.7985 (tpp) REVERT: D 120 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7930 (mm) REVERT: D 203 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: E 4 MET cc_start: 0.8069 (ppp) cc_final: 0.6847 (ppp) REVERT: E 7 LEU cc_start: 0.8806 (mt) cc_final: 0.8592 (pp) REVERT: E 150 MET cc_start: 0.8587 (tmm) cc_final: 0.8149 (tmm) outliers start: 31 outliers final: 22 residues processed: 246 average time/residue: 0.0964 time to fit residues: 33.3470 Evaluate side-chains 245 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 205 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN D 220 GLN E 218 HIS I 23 HIS K 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.150795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.116927 restraints weight = 23283.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.120844 restraints weight = 11962.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.123197 restraints weight = 8408.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.123880 restraints weight = 7054.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.124888 restraints weight = 6598.438| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10231 Z= 0.172 Angle : 0.634 13.376 13844 Z= 0.324 Chirality : 0.038 0.161 1633 Planarity : 0.003 0.038 1736 Dihedral : 3.416 17.430 1368 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 3.95 % Allowed : 21.66 % Favored : 74.40 % 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: 3.71 (0.23), residues: 1265 helix: 2.90 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.88 (0.48), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 110 TYR 0.026 0.002 TYR D 66 PHE 0.027 0.002 PHE A 213 TRP 0.007 0.001 TRP D 57 HIS 0.019 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00396 (10231) covalent geometry : angle 0.63401 (13844) hydrogen bonds : bond 0.04723 ( 920) hydrogen bonds : angle 3.62981 ( 2760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7672 (m) cc_final: 0.7386 (m) REVERT: A 72 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6719 (mttm) REVERT: A 110 ARG cc_start: 0.8585 (tmm160) cc_final: 0.8283 (ttp80) REVERT: A 154 ILE cc_start: 0.9262 (pt) cc_final: 0.9029 (mm) REVERT: A 207 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 218 HIS cc_start: 0.8639 (t70) cc_final: 0.8209 (t70) REVERT: B 12 LYS cc_start: 0.8976 (pttp) cc_final: 0.8498 (pttm) REVERT: B 67 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: B 206 TYR cc_start: 0.8715 (m-10) cc_final: 0.8493 (m-10) REVERT: B 207 ASP cc_start: 0.8640 (t0) cc_final: 0.8388 (t0) REVERT: C 84 TYR cc_start: 0.7742 (t80) cc_final: 0.7382 (t80) REVERT: C 203 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8055 (tm-30) REVERT: C 217 LEU cc_start: 0.9134 (mt) cc_final: 0.8673 (tt) REVERT: D 12 LYS cc_start: 0.8656 (tptt) cc_final: 0.8324 (tptt) REVERT: E 4 MET cc_start: 0.8167 (ppp) cc_final: 0.6941 (ppp) REVERT: E 7 LEU cc_start: 0.8849 (mt) cc_final: 0.8625 (pp) REVERT: E 150 MET cc_start: 0.8625 (tmm) cc_final: 0.8155 (tmm) outliers start: 41 outliers final: 25 residues processed: 249 average time/residue: 0.0969 time to fit residues: 33.8405 Evaluate side-chains 245 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 HIS I 8 GLN K 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.148557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.115101 restraints weight = 23208.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.117531 restraints weight = 13584.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.118464 restraints weight = 8928.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.118974 restraints weight = 8395.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119205 restraints weight = 8132.115| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10231 Z= 0.183 Angle : 0.657 16.870 13844 Z= 0.335 Chirality : 0.039 0.179 1633 Planarity : 0.003 0.033 1736 Dihedral : 3.467 17.258 1368 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 4.04 % Allowed : 22.81 % Favored : 73.15 % 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: 3.56 (0.23), residues: 1265 helix: 2.80 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.92 (0.47), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 110 TYR 0.021 0.002 TYR A 84 PHE 0.030 0.002 PHE E 87 TRP 0.041 0.001 TRP D 57 HIS 0.004 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00424 (10231) covalent geometry : angle 0.65738 (13844) hydrogen bonds : bond 0.04890 ( 920) hydrogen bonds : angle 3.70625 ( 2760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7669 (m) cc_final: 0.7377 (m) REVERT: A 72 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6855 (mttm) REVERT: A 88 LYS cc_start: 0.9026 (mtmt) cc_final: 0.8795 (mtmt) REVERT: A 110 ARG cc_start: 0.8683 (tmm160) cc_final: 0.8340 (ttp80) REVERT: A 218 HIS cc_start: 0.8803 (t70) cc_final: 0.8346 (t70) REVERT: B 67 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8658 (pm20) REVERT: B 110 ARG cc_start: 0.8042 (ptm160) cc_final: 0.6869 (ptp-170) REVERT: B 207 ASP cc_start: 0.8706 (t0) cc_final: 0.8392 (t0) REVERT: C 84 TYR cc_start: 0.7840 (t80) cc_final: 0.7361 (t80) REVERT: C 190 MET cc_start: 0.8165 (ttp) cc_final: 0.7906 (ttp) REVERT: C 203 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 217 LEU cc_start: 0.9154 (mt) cc_final: 0.8694 (tt) REVERT: D 12 LYS cc_start: 0.8809 (tptt) cc_final: 0.8419 (tptt) REVERT: D 112 MET cc_start: 0.8330 (tpp) cc_final: 0.8059 (tpp) REVERT: E 7 LEU cc_start: 0.8950 (mt) cc_final: 0.8659 (pp) REVERT: E 81 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7267 (tm-30) REVERT: E 118 ARG cc_start: 0.8522 (mtm180) cc_final: 0.8223 (mtm180) REVERT: E 150 MET cc_start: 0.8727 (tmm) cc_final: 0.8191 (tmm) REVERT: G 28 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8435 (tt) REVERT: I 8 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6928 (pm20) outliers start: 42 outliers final: 25 residues processed: 242 average time/residue: 0.0945 time to fit residues: 31.8817 Evaluate side-chains 245 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS E 218 HIS I 8 GLN K 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.150434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.116263 restraints weight = 22998.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.120077 restraints weight = 11950.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.122423 restraints weight = 8415.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.123120 restraints weight = 7072.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.124286 restraints weight = 6617.920| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10231 Z= 0.140 Angle : 0.644 15.750 13844 Z= 0.325 Chirality : 0.038 0.149 1633 Planarity : 0.003 0.033 1736 Dihedral : 3.484 17.194 1368 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.31 % Rotamer: Outliers : 3.18 % Allowed : 23.87 % Favored : 72.95 % 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: 3.72 (0.23), residues: 1265 helix: 2.90 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.79 (0.48), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 110 TYR 0.019 0.002 TYR A 84 PHE 0.027 0.001 PHE A 213 TRP 0.067 0.001 TRP D 57 HIS 0.004 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00292 (10231) covalent geometry : angle 0.64447 (13844) hydrogen bonds : bond 0.04595 ( 920) hydrogen bonds : angle 3.59328 ( 2760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7642 (m) cc_final: 0.7362 (m) REVERT: A 72 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7057 (mttm) REVERT: A 110 ARG cc_start: 0.8580 (tmm160) cc_final: 0.8270 (ttp80) REVERT: A 207 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8165 (t0) REVERT: A 218 HIS cc_start: 0.8665 (t70) cc_final: 0.8221 (t70) REVERT: B 12 LYS cc_start: 0.8924 (pttp) cc_final: 0.8428 (ptpp) REVERT: B 67 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: B 110 ARG cc_start: 0.7797 (ptm160) cc_final: 0.6947 (ptp-170) REVERT: C 4 MET cc_start: 0.2792 (mpp) cc_final: 0.2500 (mpp) REVERT: C 84 TYR cc_start: 0.7716 (t80) cc_final: 0.7321 (t80) REVERT: C 150 MET cc_start: 0.8510 (ptp) cc_final: 0.8110 (ptm) REVERT: C 190 MET cc_start: 0.8138 (ttp) cc_final: 0.7933 (ttp) REVERT: C 203 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8029 (tm-30) REVERT: C 217 LEU cc_start: 0.9119 (mt) cc_final: 0.8668 (tt) REVERT: D 12 LYS cc_start: 0.8644 (tptt) cc_final: 0.8310 (tptt) REVERT: D 35 ILE cc_start: 0.7616 (mt) cc_final: 0.7321 (mt) REVERT: D 55 LYS cc_start: 0.9273 (tptp) cc_final: 0.9038 (tppt) REVERT: D 118 ARG cc_start: 0.8015 (mtm180) cc_final: 0.7810 (mtm110) REVERT: E 7 LEU cc_start: 0.8811 (mt) cc_final: 0.8575 (pp) REVERT: E 150 MET cc_start: 0.8620 (tmm) cc_final: 0.8169 (tmm) REVERT: G 28 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8437 (tt) outliers start: 33 outliers final: 23 residues processed: 237 average time/residue: 0.1017 time to fit residues: 33.2980 Evaluate side-chains 245 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS K 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.150934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.116985 restraints weight = 23031.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.120786 restraints weight = 12065.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.123217 restraints weight = 8522.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.124180 restraints weight = 7123.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.125003 restraints weight = 6592.611| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10231 Z= 0.135 Angle : 0.642 14.961 13844 Z= 0.326 Chirality : 0.038 0.154 1633 Planarity : 0.003 0.033 1736 Dihedral : 3.457 17.486 1368 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 3.08 % Allowed : 24.16 % Favored : 72.76 % 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: 3.76 (0.23), residues: 1265 helix: 2.91 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -1.73 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 113 TYR 0.018 0.001 TYR A 84 PHE 0.029 0.001 PHE A 213 TRP 0.056 0.001 TRP D 57 HIS 0.004 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00279 (10231) covalent geometry : angle 0.64175 (13844) hydrogen bonds : bond 0.04476 ( 920) hydrogen bonds : angle 3.57965 ( 2760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7640 (m) cc_final: 0.7360 (m) REVERT: A 72 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6714 (mttm) REVERT: A 110 ARG cc_start: 0.8530 (tmm160) cc_final: 0.8214 (ttp80) REVERT: A 207 ASP cc_start: 0.8428 (t70) cc_final: 0.8143 (t0) REVERT: A 218 HIS cc_start: 0.8612 (t70) cc_final: 0.8125 (t70) REVERT: B 12 LYS cc_start: 0.8912 (pttp) cc_final: 0.8457 (pttm) REVERT: B 67 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: B 110 ARG cc_start: 0.7584 (ptm160) cc_final: 0.7246 (ptm160) REVERT: C 84 TYR cc_start: 0.7694 (t80) cc_final: 0.7330 (t80) REVERT: C 150 MET cc_start: 0.8508 (ptp) cc_final: 0.8161 (ptm) REVERT: C 203 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 217 LEU cc_start: 0.9098 (mt) cc_final: 0.8651 (tt) REVERT: D 12 LYS cc_start: 0.8632 (tptt) cc_final: 0.8306 (tptt) REVERT: D 35 ILE cc_start: 0.7672 (mt) cc_final: 0.7390 (mt) REVERT: D 87 PHE cc_start: 0.8263 (t80) cc_final: 0.7917 (t80) REVERT: E 7 LEU cc_start: 0.8776 (mt) cc_final: 0.8545 (pp) REVERT: E 150 MET cc_start: 0.8593 (tmm) cc_final: 0.8141 (tmm) REVERT: G 28 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8463 (tt) outliers start: 32 outliers final: 25 residues processed: 238 average time/residue: 0.0953 time to fit residues: 31.5186 Evaluate side-chains 247 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS I 8 GLN K 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.150373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.116217 restraints weight = 22878.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.120048 restraints weight = 11990.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.122423 restraints weight = 8522.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.123638 restraints weight = 7155.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.123926 restraints weight = 6580.167| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10231 Z= 0.149 Angle : 0.667 16.410 13844 Z= 0.338 Chirality : 0.038 0.156 1633 Planarity : 0.003 0.033 1736 Dihedral : 3.449 17.702 1368 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 3.27 % Allowed : 23.48 % 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: 3.68 (0.23), residues: 1265 helix: 2.88 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.71 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 118 TYR 0.028 0.002 TYR A 84 PHE 0.037 0.002 PHE E 87 TRP 0.047 0.001 TRP D 57 HIS 0.003 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00330 (10231) covalent geometry : angle 0.66740 (13844) hydrogen bonds : bond 0.04522 ( 920) hydrogen bonds : angle 3.62277 ( 2760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2530 Ramachandran restraints generated. 1265 Oldfield, 0 Emsley, 1265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.7620 (m) cc_final: 0.7333 (m) REVERT: A 72 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7048 (mttm) REVERT: A 110 ARG cc_start: 0.8538 (tmm160) cc_final: 0.8228 (ttp80) REVERT: A 218 HIS cc_start: 0.8626 (t70) cc_final: 0.8143 (t70) REVERT: B 12 LYS cc_start: 0.8919 (pttp) cc_final: 0.8453 (pttm) REVERT: B 67 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8603 (pm20) REVERT: B 110 ARG cc_start: 0.7363 (ptm160) cc_final: 0.6440 (ptm160) REVERT: B 116 MET cc_start: 0.9079 (ttm) cc_final: 0.8876 (ttp) REVERT: C 4 MET cc_start: 0.3057 (mpp) cc_final: 0.2706 (mpp) REVERT: C 84 TYR cc_start: 0.7705 (t80) cc_final: 0.7325 (t80) REVERT: C 150 MET cc_start: 0.8513 (ptp) cc_final: 0.8145 (ptm) REVERT: C 203 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 217 LEU cc_start: 0.9104 (mt) cc_final: 0.8643 (tt) REVERT: D 12 LYS cc_start: 0.8615 (tptt) cc_final: 0.8259 (tptt) REVERT: D 87 PHE cc_start: 0.8282 (t80) cc_final: 0.7947 (t80) REVERT: D 203 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: E 7 LEU cc_start: 0.8797 (mt) cc_final: 0.8565 (pp) REVERT: E 150 MET cc_start: 0.8596 (tmm) cc_final: 0.8149 (tmm) REVERT: G 28 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8476 (tt) outliers start: 34 outliers final: 24 residues processed: 240 average time/residue: 0.1006 time to fit residues: 33.4701 Evaluate side-chains 250 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain K residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 7 optimal weight: 0.0010 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS I 8 GLN K 8 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.150713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.116974 restraints weight = 23077.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.120764 restraints weight = 11915.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.123192 restraints weight = 8386.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.124150 restraints weight = 7010.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.125037 restraints weight = 6489.662| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10231 Z= 0.141 Angle : 0.674 16.661 13844 Z= 0.342 Chirality : 0.038 0.156 1633 Planarity : 0.003 0.033 1736 Dihedral : 3.517 23.995 1368 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 3.18 % Allowed : 24.06 % Favored : 72.76 % 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: 3.66 (0.23), residues: 1265 helix: 2.84 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -1.69 (0.50), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 110 TYR 0.037 0.002 TYR A 84 PHE 0.042 0.002 PHE E 87 TRP 0.066 0.001 TRP D 57 HIS 0.004 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00294 (10231) covalent geometry : angle 0.67375 (13844) hydrogen bonds : bond 0.04476 ( 920) hydrogen bonds : angle 3.59879 ( 2760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.38 seconds wall clock time: 31 minutes 56.10 seconds (1916.10 seconds total)