Starting phenix.real_space_refine on Wed Mar 4 18:35:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7o3v_12709/03_2026/7o3v_12709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7o3v_12709/03_2026/7o3v_12709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7o3v_12709/03_2026/7o3v_12709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7o3v_12709/03_2026/7o3v_12709.map" model { file = "/net/cci-nas-00/data/ceres_data/7o3v_12709/03_2026/7o3v_12709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7o3v_12709/03_2026/7o3v_12709.cif" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.895 sd= 3.913 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 56 5.16 5 C 9923 2.51 5 N 2771 2.21 5 O 2992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15742 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1526 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1526 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1523 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1526 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1526 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1807 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 261, 1807 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1813 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 261, 1813 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "H" Number of atoms: 1375 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 188, 1375 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1369 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "J" Number of atoms: 1751 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 260, 1751 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 252} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 93 Time building chain proxies: 3.74, per 1000 atoms: 0.24 Number of scatterers: 15742 At special positions: 0 Unit cell: (102.432, 101.365, 226.204, 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 56 16.00 O 2992 8.00 N 2771 7.00 C 9923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 689.8 milliseconds 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3898 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 32 through 65 removed outlier: 4.196A pdb=" N PHE A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.565A pdb=" N TYR A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 118 through 163 Processing helix chain 'A' and resid 167 through 219 Processing helix chain 'B' and resid 33 through 65 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.571A pdb=" N TYR B 82 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 118 through 163 Processing helix chain 'B' and resid 167 through 219 Processing helix chain 'C' and resid 33 through 65 Processing helix chain 'C' and resid 100 through 113 Processing helix chain 'C' and resid 118 through 163 Processing helix chain 'C' and resid 167 through 219 Processing helix chain 'D' and resid 33 through 65 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 118 through 163 Processing helix chain 'D' and resid 167 through 219 removed outlier: 3.804A pdb=" N LEU D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 65 Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.502A pdb=" N SER E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 163 Processing helix chain 'E' and resid 167 through 217 removed outlier: 3.612A pdb=" N ILE E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 53 removed outlier: 3.892A pdb=" N ALA F 31 " --> pdb=" O ARG F 27 " (cutoff:3.500A) Proline residue: F 34 - end of helix Processing helix chain 'F' and resid 58 through 100 removed outlier: 4.738A pdb=" N ALA F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) Proline residue: F 95 - end of helix Processing helix chain 'F' and resid 112 through 138 removed outlier: 3.698A pdb=" N PHE F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER F 138 " --> pdb=" O ALA F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 186 Proline residue: F 181 - end of helix Processing helix chain 'F' and resid 189 through 231 Processing helix chain 'F' and resid 238 through 272 Proline residue: F 261 - end of helix removed outlier: 4.135A pdb=" N GLY F 272 " --> pdb=" O ALA F 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 53 removed outlier: 3.656A pdb=" N THR G 17 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA G 18 " --> pdb=" O ASP G 14 " (cutoff:3.500A) Proline residue: G 34 - end of helix Processing helix chain 'G' and resid 59 through 99 removed outlier: 3.758A pdb=" N PHE G 63 " --> pdb=" O PRO G 59 " (cutoff:3.500A) Proline residue: G 95 - end of helix Processing helix chain 'G' and resid 113 through 138 removed outlier: 3.660A pdb=" N PHE G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 186 Proline residue: G 181 - end of helix Processing helix chain 'G' and resid 189 through 231 removed outlier: 4.001A pdb=" N GLN G 198 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TRP G 199 " --> pdb=" O PHE G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 272 Proline residue: G 261 - end of helix removed outlier: 3.557A pdb=" N GLY G 272 " --> pdb=" O ALA G 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 28 removed outlier: 3.684A pdb=" N LEU H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 138 removed outlier: 3.968A pdb=" N ALA H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE H 137 " --> pdb=" O GLU H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 185 Proline residue: H 181 - end of helix Processing helix chain 'H' and resid 186 through 189 removed outlier: 3.751A pdb=" N TRP H 189 " --> pdb=" O ALA H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 186 through 189' Processing helix chain 'H' and resid 190 through 191 No H-bonds generated for 'chain 'H' and resid 190 through 191' Processing helix chain 'H' and resid 192 through 231 removed outlier: 3.775A pdb=" N PHE H 196 " --> pdb=" O ATHR H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 272 Proline residue: H 261 - end of helix Processing helix chain 'I' and resid 5 through 21 removed outlier: 3.531A pdb=" N TYR I 20 " --> pdb=" O THR I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 31 Processing helix chain 'I' and resid 113 through 138 removed outlier: 3.545A pdb=" N PHE I 137 " --> pdb=" O GLU I 133 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 186 Proline residue: I 181 - end of helix Processing helix chain 'I' and resid 187 through 191 removed outlier: 5.006A pdb=" N GLN I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Proline residue: I 191 - end of helix No H-bonds generated for 'chain 'I' and resid 187 through 191' Processing helix chain 'I' and resid 192 through 230 Processing helix chain 'I' and resid 238 through 272 Proline residue: I 261 - end of helix removed outlier: 3.591A pdb=" N GLY I 272 " --> pdb=" O ALA I 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 53 removed outlier: 4.163A pdb=" N ALA J 30 " --> pdb=" O SER J 26 " (cutoff:3.500A) Proline residue: J 34 - end of helix removed outlier: 3.739A pdb=" N GLY J 48 " --> pdb=" O PHE J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 94 Processing helix chain 'J' and resid 95 through 99 removed outlier: 4.357A pdb=" N ALA J 99 " --> pdb=" O ASP J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 138 removed outlier: 3.820A pdb=" N PHE J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 185 Proline residue: J 181 - end of helix Processing helix chain 'J' and resid 189 through 231 removed outlier: 3.558A pdb=" N ASP J 197 " --> pdb=" O HIS J 193 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN J 198 " --> pdb=" O ARG J 194 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP J 199 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 272 Proline residue: J 261 - end of helix 1517 hydrogen bonds defined for protein. 4536 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: 2.27 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5427 1.34 - 1.46: 2131 1.46 - 1.58: 8259 1.58 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 15928 Sorted by residual: bond pdb=" CB MET E 194 " pdb=" CG MET E 194 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.15e+00 bond pdb=" CB MET C 194 " pdb=" CG MET C 194 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 3.00e+00 bond pdb=" CB PRO I 181 " pdb=" CG PRO I 181 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.45e+00 bond pdb=" CB MET G 228 " pdb=" CG MET G 228 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" CG PRO I 181 " pdb=" CD PRO I 181 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.81e+00 ... (remaining 15923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 21385 3.21 - 6.42: 132 6.42 - 9.63: 14 9.63 - 12.84: 0 12.84 - 16.05: 2 Bond angle restraints: 21533 Sorted by residual: angle pdb=" CB MET E 194 " pdb=" CG MET E 194 " pdb=" SD MET E 194 " ideal model delta sigma weight residual 112.70 96.65 16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" CB MET C 194 " pdb=" CG MET C 194 " pdb=" SD MET C 194 " ideal model delta sigma weight residual 112.70 98.23 14.47 3.00e+00 1.11e-01 2.32e+01 angle pdb=" CA PRO I 181 " pdb=" N PRO I 181 " pdb=" CD PRO I 181 " ideal model delta sigma weight residual 112.00 106.40 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" C ILE A 126 " pdb=" N GLU A 127 " pdb=" CA GLU A 127 " ideal model delta sigma weight residual 120.31 114.57 5.74 1.52e+00 4.33e-01 1.42e+01 angle pdb=" N GLU A 127 " pdb=" CA GLU A 127 " pdb=" CB GLU A 127 " ideal model delta sigma weight residual 110.28 115.82 -5.54 1.55e+00 4.16e-01 1.28e+01 ... (remaining 21528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 8559 17.68 - 35.37: 779 35.37 - 53.05: 139 53.05 - 70.73: 34 70.73 - 88.42: 13 Dihedral angle restraints: 9524 sinusoidal: 3435 harmonic: 6089 Sorted by residual: dihedral pdb=" CA SER J 138 " pdb=" C SER J 138 " pdb=" N SER J 139 " pdb=" CA SER J 139 " ideal model delta harmonic sigma weight residual 180.00 153.79 26.21 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ARG C 68 " pdb=" C ARG C 68 " pdb=" N GLY C 69 " pdb=" CA GLY C 69 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA THR G 92 " pdb=" C THR G 92 " pdb=" N THR G 93 " pdb=" CA THR G 93 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 9521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1797 0.039 - 0.078: 568 0.078 - 0.118: 107 0.118 - 0.157: 16 0.157 - 0.196: 13 Chirality restraints: 2501 Sorted by residual: chirality pdb=" CB ILE G 151 " pdb=" CA ILE G 151 " pdb=" CG1 ILE G 151 " pdb=" CG2 ILE G 151 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CB THR G 33 " pdb=" CA THR G 33 " pdb=" OG1 THR G 33 " pdb=" CG2 THR G 33 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CG LEU C 174 " pdb=" CB LEU C 174 " pdb=" CD1 LEU C 174 " pdb=" CD2 LEU C 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 2498 not shown) Planarity restraints: 2845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 180 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO I 181 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO I 181 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO I 181 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 225 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO C 226 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 180 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO J 181 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO J 181 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 181 " 0.028 5.00e-02 4.00e+02 ... (remaining 2842 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 130 2.60 - 3.17: 14524 3.17 - 3.75: 26026 3.75 - 4.32: 31762 4.32 - 4.90: 53799 Nonbonded interactions: 126241 Sorted by model distance: nonbonded pdb=" O PRO B 84 " pdb=" OH TYR E 145 " model vdw 2.022 3.040 nonbonded pdb=" OH TYR B 145 " pdb=" O PRO D 84 " model vdw 2.100 3.040 nonbonded pdb=" O GLU C 81 " pdb=" OH TYR C 99 " model vdw 2.120 3.040 nonbonded pdb=" OE2 GLU G 4 " pdb=" OG1 THR G 7 " model vdw 2.122 3.040 nonbonded pdb=" OH TYR A 145 " pdb=" O PRO C 84 " model vdw 2.191 3.040 ... (remaining 126236 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 32 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 229)) selection = (chain 'B' and (resid 32 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 229)) selection = chain 'C' selection = (chain 'D' and (resid 32 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 229)) selection = (chain 'E' and (resid 32 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 229)) } ncs_group { reference = (chain 'F' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 22 or (resid 23 and (name N or name \ CA or name C or name O or name CB )) or resid 24 through 26 or (resid 27 throug \ h 38 and (name N or name CA or name C or name O or name CB )) or (resid 39 throu \ gh 47 and (name N or name CA or name C or name O or name CB )) or resid 48 or (r \ esid 49 through 53 and (name N or name CA or name C or name O or name CB )) or ( \ resid 54 through 70 and (name N or name CA or name C or name O or name CB )) or \ (resid 71 through 84 and (name N or name CA or name C or name O or name CB )) or \ resid 85 or (resid 86 through 99 and (name N or name CA or name C or name O or \ name CB )) or (resid 112 through 115 and (name N or name CA or name C or name O \ or name CB )) or resid 116 through 117 or (resid 118 and (name N or name CA or n \ ame C or name O or name CB )) or resid 119 through 193 or (resid 194 and (name N \ or name CA or name C or name O or name CB )) or resid 195 through 229 or (resid \ 230 and (name N or name CA or name C or name O or name CB )) or resid 231 throu \ gh 270 or (resid 271 and (name N or name CA or name C or name O or name CB )) or \ resid 272)) selection = (chain 'G' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 13 or (resid 14 and (name N or name CA \ or name C or name O or name CB )) or resid 15 through 22 or (resid 23 and (name \ N or name CA or name C or name O or name CB )) or resid 24 through 28 or (resid \ 29 through 38 and (name N or name CA or name C or name O or name CB )) or (resi \ d 39 through 47 and (name N or name CA or name C or name O or name CB )) or resi \ d 48 or (resid 49 through 53 and (name N or name CA or name C or name O or name \ CB )) or (resid 54 through 70 and (name N or name CA or name C or name O or name \ CB )) or (resid 71 through 79 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 80 through 84 and (name N or name CA or name C or name O or na \ me CB )) or resid 85 through 99 or (resid 112 through 115 and (name N or name CA \ or name C or name O or name CB )) or resid 116 through 117 or (resid 118 and (n \ ame N or name CA or name C or name O or name CB )) or resid 119 through 189 or ( \ resid 190 and (name N or name CA or name C or name O or name CB )) or resid 191 \ through 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272)) selection = (chain 'J' and (resid 2 through 26 or (resid 27 through 38 and (name N or name C \ A or name C or name O or name CB )) or resid 39 through 99 or resid 112 through \ 189 or (resid 190 and (name N or name CA or name C or name O or name CB )) or re \ sid 191 through 193 or (resid 194 and (name N or name CA or name C or name O or \ name CB )) or resid 195 through 229 or (resid 230 and (name N or name CA or name \ C or name O or name CB )) or resid 231 through 272)) } ncs_group { reference = (chain 'H' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 181 or (resid 182 through 194 and (nam \ e N or name CA or name C or name O or name CB )) or resid 195 through 196 or (re \ sid 197 through 198 and (name N or name CA or name C or name O or name CB )) or \ resid 199 through 266 or (resid 267 through 268 and (name N or name CA or name C \ or name O or name CB )) or resid 269 through 270 or (resid 271 and (name N or n \ ame CA or name C or name O or name CB )) or resid 272)) selection = (chain 'I' and (resid 2 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 26 or (resid 27 through 31 and (nam \ e N or name CA or name C or name O or name CB )) or resid 115 through 272)) } 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: 0.170 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.080 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 0.004 0.078 15928 Z= 0.205 Angle : 0.712 16.048 21533 Z= 0.398 Chirality : 0.040 0.196 2501 Planarity : 0.004 0.118 2845 Dihedral : 14.439 88.416 5626 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 2.19 (0.18), residues: 2123 helix: 2.04 (0.12), residues: 1807 sheet: None (None), residues: 0 loop : -2.13 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 88 TYR 0.027 0.002 TYR E 99 PHE 0.021 0.002 PHE J 217 TRP 0.015 0.002 TRP G 189 HIS 0.002 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00429 (15928) covalent geometry : angle 0.71237 (21533) hydrogen bonds : bond 0.08559 ( 1517) hydrogen bonds : angle 4.95167 ( 4536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7536 (tt0) cc_final: 0.7309 (tt0) REVERT: B 116 ASN cc_start: 0.7191 (p0) cc_final: 0.6883 (p0) REVERT: C 122 MET cc_start: 0.8050 (mmm) cc_final: 0.7707 (tpt) REVERT: C 212 GLU cc_start: 0.8607 (tp30) cc_final: 0.8330 (tp30) REVERT: D 159 MET cc_start: 0.8425 (mmm) cc_final: 0.7928 (mmm) REVERT: E 44 LYS cc_start: 0.7274 (tppp) cc_final: 0.6794 (tppp) REVERT: E 74 MET cc_start: 0.7450 (mtt) cc_final: 0.7212 (mtp) REVERT: F 170 LYS cc_start: 0.8982 (mttt) cc_final: 0.8473 (tttt) REVERT: F 227 TYR cc_start: 0.8802 (t80) cc_final: 0.8167 (t80) REVERT: G 121 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7493 (tm-30) REVERT: G 133 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8015 (mm-30) REVERT: G 262 SER cc_start: 0.7939 (t) cc_final: 0.7739 (t) REVERT: J 126 ARG cc_start: 0.8454 (mmp-170) cc_final: 0.8184 (mmm160) REVERT: J 129 GLU cc_start: 0.7974 (mp0) cc_final: 0.7744 (mp0) REVERT: J 228 MET cc_start: 0.7471 (mmt) cc_final: 0.7131 (mmt) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.1128 time to fit residues: 87.6384 Evaluate side-chains 431 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN E 150 GLN E 197 GLN J 15 GLN J 193 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.157355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145017 restraints weight = 25696.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148075 restraints weight = 16094.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150071 restraints weight = 9171.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150820 restraints weight = 5711.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151612 restraints weight = 4577.266| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15928 Z= 0.237 Angle : 0.691 11.607 21533 Z= 0.366 Chirality : 0.040 0.198 2501 Planarity : 0.005 0.080 2845 Dihedral : 4.333 27.445 2312 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.75 % Allowed : 13.37 % Favored : 82.88 % 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: 2.16 (0.18), residues: 2123 helix: 2.03 (0.12), residues: 1807 sheet: None (None), residues: 0 loop : -2.24 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 177 TYR 0.027 0.002 TYR G 206 PHE 0.039 0.002 PHE I 213 TRP 0.015 0.002 TRP G 189 HIS 0.003 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00518 (15928) covalent geometry : angle 0.69054 (21533) hydrogen bonds : bond 0.06417 ( 1517) hydrogen bonds : angle 4.81408 ( 4536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 459 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.9049 (t80) cc_final: 0.8522 (t80) REVERT: B 59 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6364 (mtp85) REVERT: B 116 ASN cc_start: 0.7230 (p0) cc_final: 0.6978 (p0) REVERT: B 146 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: B 197 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8447 (tm-30) REVERT: C 61 TYR cc_start: 0.8127 (t80) cc_final: 0.7646 (t80) REVERT: C 212 GLU cc_start: 0.8483 (tp30) cc_final: 0.8272 (tp30) REVERT: E 44 LYS cc_start: 0.7419 (tppp) cc_final: 0.6935 (tppp) REVERT: F 170 LYS cc_start: 0.9093 (mttt) cc_final: 0.8469 (tttt) REVERT: F 227 TYR cc_start: 0.8822 (t80) cc_final: 0.8163 (t80) REVERT: G 121 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7443 (tm-30) REVERT: G 133 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7988 (mm-30) REVERT: I 23 ASP cc_start: 0.6943 (m-30) cc_final: 0.6684 (m-30) REVERT: I 213 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7577 (t80) REVERT: J 12 LYS cc_start: 0.8424 (tppt) cc_final: 0.7947 (tppt) outliers start: 55 outliers final: 34 residues processed: 479 average time/residue: 0.1176 time to fit residues: 84.5742 Evaluate side-chains 476 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 439 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 213 PHE Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN E 197 GLN J 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145891 restraints weight = 25767.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148410 restraints weight = 14823.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.150095 restraints weight = 9563.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.151260 restraints weight = 6765.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.152023 restraints weight = 5154.124| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15928 Z= 0.203 Angle : 0.642 9.780 21533 Z= 0.338 Chirality : 0.039 0.261 2501 Planarity : 0.004 0.062 2845 Dihedral : 4.252 27.462 2312 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.23 % Allowed : 17.60 % Favored : 78.17 % 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: 2.36 (0.18), residues: 2123 helix: 2.19 (0.12), residues: 1805 sheet: None (None), residues: 0 loop : -2.31 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 123 TYR 0.021 0.002 TYR D 99 PHE 0.034 0.002 PHE I 213 TRP 0.015 0.002 TRP H 199 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00435 (15928) covalent geometry : angle 0.64169 (21533) hydrogen bonds : bond 0.06242 ( 1517) hydrogen bonds : angle 4.67215 ( 4536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 464 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.9062 (t80) cc_final: 0.8568 (t80) REVERT: A 181 GLU cc_start: 0.8131 (tp30) cc_final: 0.7849 (tp30) REVERT: B 58 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7808 (mp10) REVERT: B 116 ASN cc_start: 0.7208 (p0) cc_final: 0.6973 (p0) REVERT: B 146 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: B 197 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8405 (tm-30) REVERT: C 61 TYR cc_start: 0.8133 (t80) cc_final: 0.7930 (t80) REVERT: C 122 MET cc_start: 0.7997 (mmm) cc_final: 0.7770 (mmm) REVERT: C 212 GLU cc_start: 0.8467 (tp30) cc_final: 0.8255 (tp30) REVERT: D 159 MET cc_start: 0.8562 (mmm) cc_final: 0.7968 (mmm) REVERT: D 214 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8526 (t0) REVERT: E 44 LYS cc_start: 0.7411 (tppp) cc_final: 0.6955 (tppp) REVERT: E 45 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7137 (tm-30) REVERT: E 53 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7428 (tm-30) REVERT: F 170 LYS cc_start: 0.9058 (mttt) cc_final: 0.8493 (tttt) REVERT: F 213 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: F 227 TYR cc_start: 0.8818 (t80) cc_final: 0.8192 (t80) REVERT: G 121 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7437 (tm-30) REVERT: G 133 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8021 (mm-30) REVERT: G 182 LEU cc_start: 0.8087 (mp) cc_final: 0.7877 (tt) REVERT: G 258 MET cc_start: 0.7187 (mmm) cc_final: 0.6535 (tpt) REVERT: H 258 MET cc_start: 0.8378 (mmm) cc_final: 0.7783 (mmm) REVERT: I 213 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7674 (t80) REVERT: J 222 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7412 (tm-30) outliers start: 62 outliers final: 41 residues processed: 486 average time/residue: 0.1183 time to fit residues: 86.6143 Evaluate side-chains 495 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 449 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 213 PHE Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 10 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN J 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147370 restraints weight = 25739.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149962 restraints weight = 14911.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.151874 restraints weight = 9994.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152731 restraints weight = 6292.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.153780 restraints weight = 4780.805| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15928 Z= 0.184 Angle : 0.625 10.093 21533 Z= 0.327 Chirality : 0.038 0.205 2501 Planarity : 0.004 0.058 2845 Dihedral : 4.180 27.348 2312 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.50 % Allowed : 20.60 % Favored : 74.90 % 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: 2.61 (0.18), residues: 2123 helix: 2.38 (0.12), residues: 1795 sheet: None (None), residues: 0 loop : -2.22 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 123 TYR 0.018 0.002 TYR D 99 PHE 0.031 0.002 PHE I 217 TRP 0.014 0.001 TRP H 199 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00388 (15928) covalent geometry : angle 0.62479 (21533) hydrogen bonds : bond 0.06058 ( 1517) hydrogen bonds : angle 4.55593 ( 4536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 454 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8886 (t80) cc_final: 0.8663 (t80) REVERT: A 145 TYR cc_start: 0.9037 (t80) cc_final: 0.8605 (t80) REVERT: A 181 GLU cc_start: 0.8178 (tp30) cc_final: 0.7882 (tp30) REVERT: B 58 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7818 (mp10) REVERT: B 146 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: B 197 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 128 GLU cc_start: 0.7443 (tp30) cc_final: 0.7235 (tp30) REVERT: C 212 GLU cc_start: 0.8467 (tp30) cc_final: 0.8267 (tp30) REVERT: D 159 MET cc_start: 0.8607 (mmm) cc_final: 0.8027 (mmm) REVERT: D 214 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8582 (t0) REVERT: E 44 LYS cc_start: 0.7418 (tppp) cc_final: 0.6937 (tppp) REVERT: E 45 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7520 (tm-30) REVERT: E 53 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7335 (tm-30) REVERT: F 170 LYS cc_start: 0.9076 (mttt) cc_final: 0.8479 (tttt) REVERT: F 227 TYR cc_start: 0.8847 (t80) cc_final: 0.8181 (t80) REVERT: G 133 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8041 (mm-30) REVERT: G 237 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: G 258 MET cc_start: 0.7140 (mmm) cc_final: 0.6508 (tpt) REVERT: H 258 MET cc_start: 0.8372 (mmm) cc_final: 0.7862 (mmm) REVERT: I 12 LYS cc_start: 0.8586 (tppt) cc_final: 0.8252 (tppt) REVERT: I 213 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7843 (t80) REVERT: J 12 LYS cc_start: 0.8382 (tppt) cc_final: 0.8052 (tppt) outliers start: 66 outliers final: 38 residues processed: 480 average time/residue: 0.1166 time to fit residues: 83.8034 Evaluate side-chains 491 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 448 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 137 ASP Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 213 PHE Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 117 optimal weight: 0.0000 chunk 86 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN J 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147461 restraints weight = 25635.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.150025 restraints weight = 14745.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.151698 restraints weight = 9488.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152828 restraints weight = 6700.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153610 restraints weight = 5105.513| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3898 r_free = 0.3898 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15928 Z= 0.181 Angle : 0.630 10.299 21533 Z= 0.328 Chirality : 0.038 0.179 2501 Planarity : 0.004 0.056 2845 Dihedral : 4.115 27.066 2312 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.64 % Allowed : 22.24 % Favored : 73.12 % 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: 2.66 (0.18), residues: 2123 helix: 2.43 (0.12), residues: 1796 sheet: None (None), residues: 0 loop : -2.27 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 59 TYR 0.030 0.002 TYR E 145 PHE 0.030 0.002 PHE I 213 TRP 0.013 0.001 TRP H 199 HIS 0.001 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00379 (15928) covalent geometry : angle 0.62952 (21533) hydrogen bonds : bond 0.05985 ( 1517) hydrogen bonds : angle 4.51122 ( 4536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 453 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6559 (tp30) REVERT: A 61 TYR cc_start: 0.8907 (t80) cc_final: 0.8683 (t80) REVERT: A 145 TYR cc_start: 0.9013 (t80) cc_final: 0.8598 (t80) REVERT: A 181 GLU cc_start: 0.8144 (tp30) cc_final: 0.7888 (tp30) REVERT: B 113 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 146 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: B 197 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 40 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6498 (t80) REVERT: C 61 TYR cc_start: 0.7929 (t80) cc_final: 0.7498 (t80) REVERT: C 128 GLU cc_start: 0.7443 (tp30) cc_final: 0.7241 (tp30) REVERT: C 212 GLU cc_start: 0.8460 (tp30) cc_final: 0.8250 (tp30) REVERT: C 215 MET cc_start: 0.8003 (ttm) cc_final: 0.7483 (mtp) REVERT: D 124 ARG cc_start: 0.7332 (mtm-85) cc_final: 0.7105 (mtm-85) REVERT: D 214 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8622 (t0) REVERT: E 44 LYS cc_start: 0.7401 (tppp) cc_final: 0.6924 (tppp) REVERT: E 45 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7510 (tm-30) REVERT: F 86 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: F 170 LYS cc_start: 0.9046 (mttt) cc_final: 0.8467 (tttt) REVERT: F 213 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: F 227 TYR cc_start: 0.8847 (t80) cc_final: 0.8175 (t80) REVERT: G 121 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7627 (tm-30) REVERT: G 133 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8004 (mm-30) REVERT: G 237 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: G 241 TYR cc_start: 0.8414 (m-80) cc_final: 0.8166 (m-80) REVERT: G 258 MET cc_start: 0.7114 (mmm) cc_final: 0.6492 (tpt) REVERT: H 258 MET cc_start: 0.8310 (mmm) cc_final: 0.7813 (mmm) REVERT: I 12 LYS cc_start: 0.8580 (tppt) cc_final: 0.8276 (tppt) REVERT: I 213 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7881 (t80) outliers start: 68 outliers final: 45 residues processed: 484 average time/residue: 0.1183 time to fit residues: 85.9728 Evaluate side-chains 498 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 446 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 258 MET Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 213 PHE Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 132 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.158055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145784 restraints weight = 25728.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148758 restraints weight = 15986.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150705 restraints weight = 9353.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151569 restraints weight = 5885.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.152545 restraints weight = 4580.838| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3876 r_free = 0.3876 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15928 Z= 0.204 Angle : 0.667 10.732 21533 Z= 0.346 Chirality : 0.039 0.225 2501 Planarity : 0.004 0.056 2845 Dihedral : 4.159 27.110 2312 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.84 % Allowed : 23.06 % Favored : 72.10 % 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: 2.56 (0.18), residues: 2123 helix: 2.34 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -2.27 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 114 TYR 0.023 0.002 TYR E 145 PHE 0.033 0.002 PHE F 213 TRP 0.013 0.002 TRP H 199 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00438 (15928) covalent geometry : angle 0.66697 (21533) hydrogen bonds : bond 0.06125 ( 1517) hydrogen bonds : angle 4.59684 ( 4536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 447 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6587 (tp30) REVERT: A 61 TYR cc_start: 0.8938 (t80) cc_final: 0.8627 (t80) REVERT: A 145 TYR cc_start: 0.9008 (t80) cc_final: 0.8669 (t80) REVERT: A 202 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7539 (tm-30) REVERT: B 113 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 146 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: B 197 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 40 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6626 (t80) REVERT: C 61 TYR cc_start: 0.7897 (t80) cc_final: 0.7648 (t80) REVERT: C 128 GLU cc_start: 0.7478 (tp30) cc_final: 0.7249 (tp30) REVERT: C 212 GLU cc_start: 0.8407 (tp30) cc_final: 0.8186 (tp30) REVERT: C 215 MET cc_start: 0.7983 (ttm) cc_final: 0.7411 (mtp) REVERT: D 159 MET cc_start: 0.8588 (mmm) cc_final: 0.7914 (mmt) REVERT: D 214 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8665 (t0) REVERT: E 44 LYS cc_start: 0.7381 (tppp) cc_final: 0.7072 (tppp) REVERT: E 45 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7315 (tm-30) REVERT: F 47 TYR cc_start: 0.6672 (t80) cc_final: 0.6449 (t80) REVERT: F 86 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.6259 (tt0) REVERT: F 170 LYS cc_start: 0.9049 (mttt) cc_final: 0.8463 (tttt) REVERT: F 213 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7096 (t80) REVERT: F 227 TYR cc_start: 0.8833 (t80) cc_final: 0.8162 (t80) REVERT: G 121 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7617 (tm-30) REVERT: G 133 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7997 (mm-30) REVERT: G 228 MET cc_start: 0.8616 (ttm) cc_final: 0.8338 (ttm) REVERT: G 237 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: G 241 TYR cc_start: 0.8378 (m-80) cc_final: 0.8114 (m-80) REVERT: G 258 MET cc_start: 0.7151 (mmm) cc_final: 0.6499 (tpt) REVERT: H 5 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7574 (tp) REVERT: H 24 ILE cc_start: 0.5180 (OUTLIER) cc_final: 0.4078 (tp) REVERT: H 258 MET cc_start: 0.8240 (mmm) cc_final: 0.7811 (mmm) REVERT: I 12 LYS cc_start: 0.8619 (tppt) cc_final: 0.8235 (tppt) REVERT: I 213 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7875 (t80) REVERT: J 12 LYS cc_start: 0.8465 (tppt) cc_final: 0.8180 (tppt) outliers start: 71 outliers final: 46 residues processed: 479 average time/residue: 0.1198 time to fit residues: 85.5044 Evaluate side-chains 495 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 440 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 213 PHE Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 70 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 80 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 175 GLN E 182 GLN E 197 GLN F 84 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.164287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151865 restraints weight = 25332.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154579 restraints weight = 14181.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156360 restraints weight = 8998.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.157566 restraints weight = 6272.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.158331 restraints weight = 4715.223| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15928 Z= 0.151 Angle : 0.627 10.106 21533 Z= 0.320 Chirality : 0.038 0.218 2501 Planarity : 0.004 0.055 2845 Dihedral : 4.007 26.033 2312 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.27 % Allowed : 25.85 % Favored : 70.87 % 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: 2.87 (0.18), residues: 2123 helix: 2.55 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -2.15 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 114 TYR 0.020 0.002 TYR E 145 PHE 0.029 0.002 PHE F 213 TRP 0.018 0.002 TRP F 189 HIS 0.001 0.000 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00293 (15928) covalent geometry : angle 0.62738 (21533) hydrogen bonds : bond 0.05541 ( 1517) hydrogen bonds : angle 4.29660 ( 4536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 455 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6628 (tp30) REVERT: A 61 TYR cc_start: 0.8859 (t80) cc_final: 0.8578 (t80) REVERT: A 145 TYR cc_start: 0.8931 (t80) cc_final: 0.8578 (t80) REVERT: A 198 LEU cc_start: 0.9190 (tt) cc_final: 0.8892 (tp) REVERT: A 214 ASN cc_start: 0.9004 (t0) cc_final: 0.8763 (t0) REVERT: B 113 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 197 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8349 (tm-30) REVERT: C 40 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6357 (t80) REVERT: C 59 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7224 (ttp-110) REVERT: C 61 TYR cc_start: 0.8005 (t80) cc_final: 0.7706 (t80) REVERT: C 122 MET cc_start: 0.7942 (mmm) cc_final: 0.7738 (tpp) REVERT: D 145 TYR cc_start: 0.8483 (t80) cc_final: 0.8238 (t80) REVERT: D 159 MET cc_start: 0.8624 (mmm) cc_final: 0.7743 (mmt) REVERT: E 44 LYS cc_start: 0.7276 (tppp) cc_final: 0.6866 (tppp) REVERT: E 45 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7309 (tp30) REVERT: E 53 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7230 (tm-30) REVERT: E 202 GLU cc_start: 0.8415 (tp30) cc_final: 0.8189 (tt0) REVERT: F 86 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6146 (tt0) REVERT: F 170 LYS cc_start: 0.9035 (mttt) cc_final: 0.8452 (tttt) REVERT: F 192 THR cc_start: 0.6897 (OUTLIER) cc_final: 0.6469 (p) REVERT: F 213 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7076 (t80) REVERT: F 227 TYR cc_start: 0.8859 (t80) cc_final: 0.8203 (t80) REVERT: G 121 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7682 (tm-30) REVERT: G 133 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7854 (mm-30) REVERT: G 227 TYR cc_start: 0.8623 (t80) cc_final: 0.8320 (t80) REVERT: G 258 MET cc_start: 0.7029 (mmm) cc_final: 0.6423 (tpt) REVERT: H 24 ILE cc_start: 0.5036 (OUTLIER) cc_final: 0.3999 (tp) REVERT: H 258 MET cc_start: 0.8178 (mmm) cc_final: 0.7779 (mmm) REVERT: I 12 LYS cc_start: 0.8538 (tppt) cc_final: 0.8139 (tppt) outliers start: 48 outliers final: 26 residues processed: 475 average time/residue: 0.1247 time to fit residues: 87.0316 Evaluate side-chains 474 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 443 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 250 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 204 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.162185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150441 restraints weight = 25674.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153523 restraints weight = 15683.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155052 restraints weight = 9203.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.155754 restraints weight = 6218.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156739 restraints weight = 4897.630| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15928 Z= 0.175 Angle : 0.667 12.301 21533 Z= 0.339 Chirality : 0.039 0.216 2501 Planarity : 0.004 0.055 2845 Dihedral : 3.997 25.860 2312 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.86 % Allowed : 26.81 % Favored : 70.33 % 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: 2.87 (0.18), residues: 2123 helix: 2.53 (0.12), residues: 1803 sheet: None (None), residues: 0 loop : -2.08 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 114 TYR 0.021 0.002 TYR D 99 PHE 0.035 0.002 PHE I 213 TRP 0.021 0.002 TRP F 189 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00372 (15928) covalent geometry : angle 0.66710 (21533) hydrogen bonds : bond 0.05655 ( 1517) hydrogen bonds : angle 4.38769 ( 4536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 449 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6734 (tp30) REVERT: A 61 TYR cc_start: 0.8917 (t80) cc_final: 0.8646 (t80) REVERT: A 145 TYR cc_start: 0.8989 (t80) cc_final: 0.8651 (t80) REVERT: A 198 LEU cc_start: 0.9257 (tt) cc_final: 0.8960 (tp) REVERT: A 214 ASN cc_start: 0.8998 (t0) cc_final: 0.8767 (t0) REVERT: B 113 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7959 (tm-30) REVERT: B 145 TYR cc_start: 0.8936 (t80) cc_final: 0.8462 (t80) REVERT: B 197 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8486 (tm-30) REVERT: C 59 ARG cc_start: 0.7554 (ttp-110) cc_final: 0.7351 (ttp-110) REVERT: C 61 TYR cc_start: 0.8041 (t80) cc_final: 0.7837 (t80) REVERT: C 122 MET cc_start: 0.8027 (mmm) cc_final: 0.7780 (tpp) REVERT: C 167 ASP cc_start: 0.7775 (m-30) cc_final: 0.7372 (t0) REVERT: D 78 GLN cc_start: 0.7906 (pm20) cc_final: 0.7637 (pp30) REVERT: D 95 ASN cc_start: 0.7977 (p0) cc_final: 0.7702 (p0) REVERT: D 159 MET cc_start: 0.8784 (mmm) cc_final: 0.7881 (mmt) REVERT: E 44 LYS cc_start: 0.7240 (tppp) cc_final: 0.6962 (tppp) REVERT: E 45 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7314 (tp30) REVERT: E 53 GLN cc_start: 0.7618 (tm-30) cc_final: 0.7274 (tm-30) REVERT: E 202 GLU cc_start: 0.8439 (tp30) cc_final: 0.8220 (tt0) REVERT: F 170 LYS cc_start: 0.9039 (mttt) cc_final: 0.8428 (tttt) REVERT: F 192 THR cc_start: 0.6776 (OUTLIER) cc_final: 0.6375 (p) REVERT: F 213 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: F 227 TYR cc_start: 0.8944 (t80) cc_final: 0.8234 (t80) REVERT: G 121 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7674 (tm-30) REVERT: G 133 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7902 (mm-30) REVERT: G 258 MET cc_start: 0.7092 (mmm) cc_final: 0.6468 (tpt) REVERT: H 24 ILE cc_start: 0.5140 (OUTLIER) cc_final: 0.4082 (tp) REVERT: H 258 MET cc_start: 0.8206 (mmm) cc_final: 0.7829 (mmm) REVERT: I 12 LYS cc_start: 0.8587 (tppt) cc_final: 0.8149 (tppt) REVERT: J 12 LYS cc_start: 0.8539 (tppt) cc_final: 0.8261 (tppt) outliers start: 42 outliers final: 31 residues processed: 472 average time/residue: 0.1228 time to fit residues: 85.0420 Evaluate side-chains 474 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 440 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 49 TRP Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 250 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 64 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.161961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149732 restraints weight = 25387.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152882 restraints weight = 15522.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154690 restraints weight = 8920.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155469 restraints weight = 5785.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156610 restraints weight = 4555.807| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15928 Z= 0.178 Angle : 0.677 10.721 21533 Z= 0.347 Chirality : 0.039 0.216 2501 Planarity : 0.004 0.099 2845 Dihedral : 4.042 25.428 2312 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.41 % Allowed : 26.47 % Favored : 70.12 % 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: 2.78 (0.18), residues: 2123 helix: 2.46 (0.12), residues: 1803 sheet: None (None), residues: 0 loop : -2.04 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 232 TYR 0.032 0.002 TYR C 145 PHE 0.034 0.002 PHE I 213 TRP 0.018 0.002 TRP F 189 HIS 0.002 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00377 (15928) covalent geometry : angle 0.67733 (21533) hydrogen bonds : bond 0.05714 ( 1517) hydrogen bonds : angle 4.42502 ( 4536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 449 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6624 (tp30) REVERT: A 91 TYR cc_start: 0.8127 (m-80) cc_final: 0.7661 (m-80) REVERT: A 145 TYR cc_start: 0.8967 (t80) cc_final: 0.8619 (t80) REVERT: A 198 LEU cc_start: 0.9239 (tt) cc_final: 0.8923 (tp) REVERT: B 113 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7927 (tm-30) REVERT: C 40 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6580 (t80) REVERT: C 61 TYR cc_start: 0.7956 (t80) cc_final: 0.7748 (t80) REVERT: C 122 MET cc_start: 0.7945 (mmm) cc_final: 0.7724 (tpp) REVERT: C 167 ASP cc_start: 0.7682 (m-30) cc_final: 0.7359 (t0) REVERT: D 78 GLN cc_start: 0.7831 (pm20) cc_final: 0.7624 (pp30) REVERT: D 95 ASN cc_start: 0.7913 (p0) cc_final: 0.7635 (p0) REVERT: D 159 MET cc_start: 0.8787 (mmm) cc_final: 0.7979 (mmt) REVERT: E 44 LYS cc_start: 0.7202 (tppp) cc_final: 0.6978 (tppp) REVERT: E 45 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7187 (tp30) REVERT: E 53 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7247 (tm-30) REVERT: E 202 GLU cc_start: 0.8368 (tp30) cc_final: 0.8005 (tt0) REVERT: F 86 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6047 (tt0) REVERT: F 170 LYS cc_start: 0.9051 (mttt) cc_final: 0.8420 (tttt) REVERT: F 192 THR cc_start: 0.6745 (OUTLIER) cc_final: 0.6327 (p) REVERT: F 213 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: F 227 TYR cc_start: 0.8866 (t80) cc_final: 0.8171 (t80) REVERT: G 3 PHE cc_start: 0.8091 (t80) cc_final: 0.7827 (t80) REVERT: G 121 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7745 (tm-30) REVERT: G 133 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7827 (mm-30) REVERT: G 227 TYR cc_start: 0.8660 (t80) cc_final: 0.8416 (t80) REVERT: G 258 MET cc_start: 0.7065 (mmm) cc_final: 0.6434 (tpt) REVERT: H 24 ILE cc_start: 0.5188 (OUTLIER) cc_final: 0.4125 (tp) REVERT: H 258 MET cc_start: 0.8127 (mmm) cc_final: 0.7741 (mmm) REVERT: I 12 LYS cc_start: 0.8554 (tppt) cc_final: 0.8149 (tppt) outliers start: 50 outliers final: 35 residues processed: 473 average time/residue: 0.1182 time to fit residues: 83.2869 Evaluate side-chains 486 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 446 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 200 GLN Chi-restraints excluded: chain F residue 49 TRP Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 250 SER Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 87 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.145946 restraints weight = 25500.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148576 restraints weight = 15678.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150575 restraints weight = 9530.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151343 restraints weight = 6033.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152333 restraints weight = 4767.018| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15928 Z= 0.236 Angle : 0.747 14.046 21533 Z= 0.388 Chirality : 0.041 0.228 2501 Planarity : 0.005 0.113 2845 Dihedral : 4.208 25.650 2312 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.62 % Allowed : 26.88 % Favored : 69.51 % 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: 2.43 (0.18), residues: 2123 helix: 2.23 (0.12), residues: 1808 sheet: None (None), residues: 0 loop : -2.30 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 124 TYR 0.025 0.002 TYR C 145 PHE 0.041 0.002 PHE I 213 TRP 0.020 0.002 TRP F 189 HIS 0.003 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00520 (15928) covalent geometry : angle 0.74675 (21533) hydrogen bonds : bond 0.06247 ( 1517) hydrogen bonds : angle 4.70880 ( 4536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 456 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6594 (tp30) REVERT: A 145 TYR cc_start: 0.8974 (t80) cc_final: 0.8595 (t80) REVERT: A 198 LEU cc_start: 0.9257 (tt) cc_final: 0.8894 (tp) REVERT: A 202 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7580 (tm-30) REVERT: B 113 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 43 MET cc_start: 0.6799 (mtm) cc_final: 0.6528 (mtm) REVERT: C 61 TYR cc_start: 0.7969 (t80) cc_final: 0.7751 (t80) REVERT: C 167 ASP cc_start: 0.7928 (m-30) cc_final: 0.7655 (t0) REVERT: D 95 ASN cc_start: 0.7934 (p0) cc_final: 0.7647 (p0) REVERT: D 159 MET cc_start: 0.8737 (mmm) cc_final: 0.8196 (mmm) REVERT: D 208 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7152 (tm-30) REVERT: E 45 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7304 (tp30) REVERT: E 53 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 202 GLU cc_start: 0.8386 (tp30) cc_final: 0.8090 (tt0) REVERT: F 86 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6186 (tt0) REVERT: F 170 LYS cc_start: 0.9042 (mttt) cc_final: 0.8438 (tttt) REVERT: F 213 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7074 (t80) REVERT: F 227 TYR cc_start: 0.8864 (t80) cc_final: 0.8042 (t80) REVERT: G 3 PHE cc_start: 0.8153 (t80) cc_final: 0.7942 (t80) REVERT: G 133 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7911 (mm-30) REVERT: G 232 ARG cc_start: 0.7324 (mtm110) cc_final: 0.7111 (ptm160) REVERT: G 258 MET cc_start: 0.7099 (mmm) cc_final: 0.6457 (tpt) REVERT: H 24 ILE cc_start: 0.5385 (OUTLIER) cc_final: 0.4200 (tp) REVERT: I 12 LYS cc_start: 0.8629 (tppt) cc_final: 0.8235 (tppt) REVERT: I 219 LEU cc_start: 0.8760 (tp) cc_final: 0.8534 (tp) outliers start: 53 outliers final: 39 residues processed: 479 average time/residue: 0.1153 time to fit residues: 83.3395 Evaluate side-chains 488 residues out of total 1659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 446 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 58 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain F residue 49 TRP Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 213 PHE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 6 PHE Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 250 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain J residue 119 SER Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 107 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 190 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.179026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164669 restraints weight = 26068.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.168039 restraints weight = 13492.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.170161 restraints weight = 8116.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.171469 restraints weight = 5465.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.172406 restraints weight = 4093.741| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4195 r_free = 0.4195 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15928 Z= 0.172 Angle : 0.713 10.922 21533 Z= 0.361 Chirality : 0.040 0.377 2501 Planarity : 0.004 0.082 2845 Dihedral : 4.112 25.115 2312 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.00 % Allowed : 28.10 % Favored : 68.89 % 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: 2.63 (0.18), residues: 2123 helix: 2.36 (0.12), residues: 1808 sheet: None (None), residues: 0 loop : -2.19 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 232 TYR 0.030 0.002 TYR C 145 PHE 0.034 0.002 PHE I 213 TRP 0.021 0.002 TRP F 189 HIS 0.001 0.001 HIS F 193 Details of bonding type rmsd covalent geometry : bond 0.00358 (15928) covalent geometry : angle 0.71331 (21533) hydrogen bonds : bond 0.05851 ( 1517) hydrogen bonds : angle 4.45075 ( 4536) =============================================================================== Job complete usr+sys time: 2613.80 seconds wall clock time: 45 minutes 41.44 seconds (2741.44 seconds total)