Starting phenix.real_space_refine on Fri Sep 27 09:19:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3v_12709/09_2024/7o3v_12709.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3v_12709/09_2024/7o3v_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3v_12709/09_2024/7o3v_12709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3v_12709/09_2024/7o3v_12709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3v_12709/09_2024/7o3v_12709.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o3v_12709/09_2024/7o3v_12709.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} 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, 'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 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: {'GLN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 93 Time building chain proxies: 9.36, per 1000 atoms: 0.59 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: 4.50 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.10 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: 4.44 Time building geometry restraints manager: 5.08 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: 0.200 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 35.460 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.050 ------------------------------------------------------------------------------- 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= 0.284 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 : 11.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (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 TRP 0.015 0.002 TRP G 189 HIS 0.002 0.001 HIS J 193 PHE 0.021 0.002 PHE J 217 TYR 0.027 0.002 TYR E 99 ARG 0.009 0.001 ARG D 88 *********************** 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 fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 2.165 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: 0.2746 time to fit residues: 209.7241 Evaluate side-chains 431 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 190 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 H 118 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15928 Z= 0.314 Angle : 0.672 11.436 21533 Z= 0.355 Chirality : 0.040 0.202 2501 Planarity : 0.005 0.083 2845 Dihedral : 4.290 27.272 2312 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.48 % Allowed : 13.37 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.18), residues: 2123 helix: 2.13 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -2.29 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 199 HIS 0.003 0.001 HIS F 193 PHE 0.036 0.002 PHE I 213 TYR 0.030 0.002 TYR D 99 ARG 0.007 0.001 ARG A 177 *********************** 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 519 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 468 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.9015 (t80) cc_final: 0.8530 (t80) REVERT: B 116 ASN cc_start: 0.7236 (p0) cc_final: 0.6989 (p0) REVERT: B 146 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6821 (tt0) REVERT: C 61 TYR cc_start: 0.8096 (t80) cc_final: 0.7885 (t80) REVERT: E 44 LYS cc_start: 0.7424 (tppp) cc_final: 0.6943 (tppp) REVERT: F 170 LYS cc_start: 0.9054 (mttt) cc_final: 0.8539 (tttt) REVERT: F 227 TYR cc_start: 0.8784 (t80) cc_final: 0.8155 (t80) REVERT: G 121 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7452 (tm-30) REVERT: G 133 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7961 (mm-30) REVERT: G 258 MET cc_start: 0.7098 (mmm) cc_final: 0.6483 (tpt) REVERT: H 258 MET cc_start: 0.8285 (mmm) cc_final: 0.8069 (mmm) REVERT: I 213 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7591 (t80) REVERT: J 12 LYS cc_start: 0.8431 (tppt) cc_final: 0.7931 (tppt) outliers start: 51 outliers final: 32 residues processed: 485 average time/residue: 0.2631 time to fit residues: 188.1246 Evaluate side-chains 484 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 450 time to evaluate : 1.830 ------------------------------------------------------------------------------- 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 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 128 SER Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 179 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 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 105 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 191 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN E 197 GLN H 118 GLN J 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.003 0.042 15928 Z= 0.204 Angle : 0.596 9.436 21533 Z= 0.310 Chirality : 0.037 0.249 2501 Planarity : 0.004 0.060 2845 Dihedral : 4.108 26.686 2312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.34 % Allowed : 17.74 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.18), residues: 2123 helix: 2.45 (0.12), residues: 1801 sheet: None (None), residues: 0 loop : -2.13 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 199 HIS 0.001 0.000 HIS F 193 PHE 0.031 0.002 PHE I 213 TYR 0.022 0.002 TYR D 99 ARG 0.006 0.000 ARG A 123 *********************** 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 519 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 470 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6513 (tp30) REVERT: A 145 TYR cc_start: 0.9002 (t80) cc_final: 0.8478 (t80) REVERT: A 181 GLU cc_start: 0.7986 (tp30) cc_final: 0.7749 (tp30) REVERT: B 58 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: B 116 ASN cc_start: 0.7125 (p0) cc_final: 0.6895 (p0) REVERT: B 146 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: B 198 LEU cc_start: 0.9096 (tt) cc_final: 0.8859 (tp) REVERT: C 122 MET cc_start: 0.7871 (mmm) cc_final: 0.7633 (tpp) REVERT: C 146 GLU cc_start: 0.7236 (mp0) cc_final: 0.7007 (mm-30) REVERT: D 159 MET cc_start: 0.8517 (mmm) cc_final: 0.7826 (mmm) REVERT: D 214 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8422 (t0) REVERT: E 44 LYS cc_start: 0.7336 (tppp) cc_final: 0.6894 (tppp) REVERT: E 53 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7349 (tm-30) REVERT: F 170 LYS cc_start: 0.9028 (mttt) cc_final: 0.8547 (tttt) REVERT: F 213 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6334 (m-80) REVERT: F 227 TYR cc_start: 0.8782 (t80) cc_final: 0.8204 (t80) REVERT: G 121 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7545 (tm-30) REVERT: G 133 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7885 (mm-30) REVERT: G 258 MET cc_start: 0.7049 (mmm) cc_final: 0.6461 (tpt) REVERT: H 258 MET cc_start: 0.7996 (mmm) cc_final: 0.7790 (mmm) REVERT: I 12 LYS cc_start: 0.8517 (tppt) cc_final: 0.8190 (tppt) REVERT: I 213 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.7743 (t80) outliers start: 49 outliers final: 28 residues processed: 489 average time/residue: 0.2630 time to fit residues: 190.2099 Evaluate side-chains 486 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 453 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 137 ASP Chi-restraints excluded: chain D residue 138 LYS Chi-restraints excluded: chain D residue 214 ASN 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 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 210 ILE Chi-restraints excluded: chain H residue 250 SER 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 188 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1902 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= 0.263 Angle : 0.636 9.820 21533 Z= 0.330 Chirality : 0.038 0.171 2501 Planarity : 0.004 0.064 2845 Dihedral : 4.090 26.546 2312 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.37 % Allowed : 20.12 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.18), residues: 2123 helix: 2.46 (0.12), residues: 1794 sheet: None (None), residues: 0 loop : -2.23 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 189 HIS 0.002 0.001 HIS F 193 PHE 0.030 0.002 PHE I 213 TYR 0.019 0.002 TYR D 99 ARG 0.008 0.000 ARG B 59 *********************** 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 522 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 458 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6611 (tp30) REVERT: A 145 TYR cc_start: 0.9010 (t80) cc_final: 0.8608 (t80) REVERT: A 181 GLU cc_start: 0.8095 (tp30) cc_final: 0.7827 (tp30) REVERT: A 192 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9205 (mm) REVERT: B 116 ASN cc_start: 0.7195 (p0) cc_final: 0.6949 (p0) REVERT: B 146 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: C 61 TYR cc_start: 0.7906 (t80) cc_final: 0.7445 (t80) REVERT: C 128 GLU cc_start: 0.7428 (tp30) cc_final: 0.7225 (tp30) REVERT: C 146 GLU cc_start: 0.7347 (mp0) cc_final: 0.7089 (mm-30) REVERT: C 212 GLU cc_start: 0.8354 (tp30) cc_final: 0.8125 (tp30) REVERT: D 95 ASN cc_start: 0.7856 (p0) cc_final: 0.7648 (p0) REVERT: D 159 MET cc_start: 0.8717 (mmm) cc_final: 0.8155 (mmm) REVERT: D 214 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8572 (t0) REVERT: E 44 LYS cc_start: 0.7371 (tppp) cc_final: 0.6900 (tppp) REVERT: E 45 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7546 (tm-30) REVERT: E 53 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7419 (tm-30) REVERT: F 170 LYS cc_start: 0.9047 (mttt) cc_final: 0.8548 (tttt) REVERT: F 227 TYR cc_start: 0.8827 (t80) cc_final: 0.8201 (t80) REVERT: G 121 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7672 (tm-30) REVERT: G 133 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7958 (mm-30) REVERT: G 258 MET cc_start: 0.7085 (mmm) cc_final: 0.6457 (tpt) REVERT: I 12 LYS cc_start: 0.8571 (tppt) cc_final: 0.8333 (tppt) REVERT: I 213 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7712 (t80) REVERT: J 12 LYS cc_start: 0.8379 (tppt) cc_final: 0.8090 (tppt) outliers start: 64 outliers final: 46 residues processed: 485 average time/residue: 0.2611 time to fit residues: 187.1142 Evaluate side-chains 498 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 448 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 87 LEU 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 192 LEU 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 64 VAL Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 74 MET 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 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 67 CYS Chi-restraints excluded: chain G residue 128 SER 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 210 ILE Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 250 SER Chi-restraints excluded: chain I residue 22 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15928 Z= 0.271 Angle : 0.641 9.560 21533 Z= 0.334 Chirality : 0.039 0.187 2501 Planarity : 0.004 0.057 2845 Dihedral : 4.104 26.532 2312 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.18 % Allowed : 21.42 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.18), residues: 2123 helix: 2.42 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -2.20 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 199 HIS 0.002 0.001 HIS F 193 PHE 0.038 0.002 PHE G 213 TYR 0.028 0.002 TYR E 145 ARG 0.006 0.000 ARG D 114 *********************** 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 526 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 450 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6653 (tp30) REVERT: A 122 MET cc_start: 0.7737 (ptp) cc_final: 0.7516 (ptp) REVERT: A 145 TYR cc_start: 0.9017 (t80) cc_final: 0.8667 (t80) REVERT: A 181 GLU cc_start: 0.8123 (tp30) cc_final: 0.7865 (tp30) REVERT: A 202 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7471 (tm-30) REVERT: B 60 MET cc_start: 0.8757 (tpp) cc_final: 0.8376 (tpp) REVERT: B 116 ASN cc_start: 0.7134 (p0) cc_final: 0.6913 (p0) REVERT: B 146 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6887 (tt0) REVERT: B 159 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8181 (mmt) REVERT: C 40 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6516 (t80) REVERT: C 43 MET cc_start: 0.7232 (mtm) cc_final: 0.6567 (mtm) REVERT: C 61 TYR cc_start: 0.7866 (t80) cc_final: 0.7646 (t80) REVERT: C 128 GLU cc_start: 0.7420 (tp30) cc_final: 0.7213 (tp30) REVERT: C 146 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: C 212 GLU cc_start: 0.8317 (tp30) cc_final: 0.8061 (tp30) REVERT: D 214 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8616 (t0) REVERT: E 44 LYS cc_start: 0.7309 (tppp) cc_final: 0.6895 (tppp) REVERT: E 45 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7255 (tm-30) REVERT: E 53 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7310 (tm-30) REVERT: E 166 GLN cc_start: 0.7025 (mp10) cc_final: 0.6636 (mp10) REVERT: F 170 LYS cc_start: 0.9001 (mttt) cc_final: 0.8536 (tttt) REVERT: F 221 MET cc_start: 0.7917 (mmm) cc_final: 0.7662 (mmt) REVERT: F 227 TYR cc_start: 0.8835 (t80) cc_final: 0.8187 (t80) REVERT: G 121 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7675 (tm-30) REVERT: G 133 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7947 (mm-30) REVERT: G 241 TYR cc_start: 0.8315 (m-80) cc_final: 0.7937 (m-80) REVERT: G 258 MET cc_start: 0.7030 (mmm) cc_final: 0.6466 (tpt) REVERT: H 5 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7613 (tp) REVERT: H 24 ILE cc_start: 0.5032 (OUTLIER) cc_final: 0.3974 (tp) REVERT: H 258 MET cc_start: 0.8080 (mmm) cc_final: 0.7667 (mmm) REVERT: I 12 LYS cc_start: 0.8595 (tppt) cc_final: 0.8177 (tppt) REVERT: I 213 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7977 (t80) outliers start: 76 outliers final: 49 residues processed: 483 average time/residue: 0.2591 time to fit residues: 184.9041 Evaluate side-chains 491 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 434 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 87 LEU 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 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 B residue 159 MET Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 74 MET 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 E residue 200 GLN 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 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 173 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 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 150 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 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 68 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 203 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2211 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= 0.245 Angle : 0.642 10.026 21533 Z= 0.333 Chirality : 0.039 0.222 2501 Planarity : 0.004 0.056 2845 Dihedral : 4.074 26.462 2312 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.57 % Allowed : 22.71 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.18), residues: 2123 helix: 2.43 (0.12), residues: 1802 sheet: None (None), residues: 0 loop : -2.18 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 199 HIS 0.001 0.001 HIS F 193 PHE 0.030 0.002 PHE G 213 TYR 0.024 0.002 TYR E 145 ARG 0.007 0.000 ARG D 114 *********************** 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 505 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 438 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6656 (tp30) REVERT: A 145 TYR cc_start: 0.8999 (t80) cc_final: 0.8664 (t80) REVERT: A 181 GLU cc_start: 0.8094 (tp30) cc_final: 0.7841 (tp30) REVERT: B 60 MET cc_start: 0.8731 (tpp) cc_final: 0.8346 (tpp) REVERT: B 116 ASN cc_start: 0.7151 (p0) cc_final: 0.6938 (p0) REVERT: B 146 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6913 (tt0) REVERT: B 159 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8079 (mmt) REVERT: C 40 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6444 (t80) REVERT: C 61 TYR cc_start: 0.8007 (t80) cc_final: 0.7773 (t80) REVERT: C 146 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: C 212 GLU cc_start: 0.8265 (tp30) cc_final: 0.8049 (tp30) REVERT: C 223 GLN cc_start: 0.8721 (tp40) cc_final: 0.8516 (tp40) REVERT: D 159 MET cc_start: 0.8582 (mmm) cc_final: 0.7883 (mmt) REVERT: D 214 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8635 (t0) REVERT: E 44 LYS cc_start: 0.7351 (tppp) cc_final: 0.6886 (tppp) REVERT: E 45 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7237 (tm-30) REVERT: E 53 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7265 (tm-30) REVERT: E 159 MET cc_start: 0.7854 (mmp) cc_final: 0.7507 (mmp) REVERT: F 86 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.6126 (tt0) REVERT: F 170 LYS cc_start: 0.9002 (mttt) cc_final: 0.8532 (tttt) REVERT: F 221 MET cc_start: 0.7917 (mmm) cc_final: 0.7672 (mmt) REVERT: F 227 TYR cc_start: 0.8843 (t80) cc_final: 0.8183 (t80) REVERT: G 121 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7667 (tm-30) REVERT: G 133 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7923 (mm-30) REVERT: G 228 MET cc_start: 0.8534 (ttm) cc_final: 0.8247 (ttm) REVERT: G 241 TYR cc_start: 0.8330 (m-80) cc_final: 0.7940 (m-80) REVERT: G 258 MET cc_start: 0.7017 (mmm) cc_final: 0.6472 (tpt) REVERT: H 5 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7521 (tp) REVERT: H 24 ILE cc_start: 0.4987 (OUTLIER) cc_final: 0.3948 (tp) REVERT: H 258 MET cc_start: 0.8077 (mmm) cc_final: 0.7728 (mmm) REVERT: I 12 LYS cc_start: 0.8589 (tppt) cc_final: 0.8201 (tppt) REVERT: I 213 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7879 (t80) REVERT: J 12 LYS cc_start: 0.8545 (tppt) cc_final: 0.8245 (tppt) outliers start: 67 outliers final: 50 residues processed: 473 average time/residue: 0.2554 time to fit residues: 178.2669 Evaluate side-chains 492 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 433 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 87 LEU 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 B residue 159 MET 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 146 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 74 MET 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 86 GLU 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 262 SER 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 128 SER 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15928 Z= 0.290 Angle : 0.672 10.269 21533 Z= 0.351 Chirality : 0.040 0.214 2501 Planarity : 0.004 0.056 2845 Dihedral : 4.149 26.426 2312 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.84 % Allowed : 23.60 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.18), residues: 2123 helix: 2.33 (0.12), residues: 1807 sheet: None (None), residues: 0 loop : -2.32 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 199 HIS 0.002 0.001 HIS F 193 PHE 0.030 0.002 PHE I 213 TYR 0.020 0.002 TYR D 99 ARG 0.007 0.000 ARG D 114 *********************** 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 504 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 433 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6686 (tp30) REVERT: A 145 TYR cc_start: 0.9000 (t80) cc_final: 0.8637 (t80) REVERT: B 60 MET cc_start: 0.8745 (tpp) cc_final: 0.8350 (tpp) REVERT: B 116 ASN cc_start: 0.7237 (p0) cc_final: 0.7024 (p0) REVERT: B 146 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: C 40 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6595 (t80) REVERT: C 43 MET cc_start: 0.7216 (mtm) cc_final: 0.6490 (mtt) REVERT: C 61 TYR cc_start: 0.8040 (t80) cc_final: 0.7805 (t80) REVERT: C 146 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: C 212 GLU cc_start: 0.8260 (tp30) cc_final: 0.8050 (tp30) REVERT: D 159 MET cc_start: 0.8672 (mmm) cc_final: 0.8073 (mmm) REVERT: D 214 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8695 (t0) REVERT: E 44 LYS cc_start: 0.7334 (tppp) cc_final: 0.7036 (tppp) REVERT: E 45 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7362 (tm-30) REVERT: E 53 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7331 (tm-30) REVERT: E 159 MET cc_start: 0.8054 (mmp) cc_final: 0.7611 (mmp) REVERT: E 202 GLU cc_start: 0.8402 (tp30) cc_final: 0.8112 (tt0) REVERT: F 47 TYR cc_start: 0.6643 (t80) cc_final: 0.6353 (t80) REVERT: F 86 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6132 (tt0) REVERT: F 170 LYS cc_start: 0.8996 (mttt) cc_final: 0.8517 (tttt) REVERT: F 221 MET cc_start: 0.7928 (mmm) cc_final: 0.7704 (mmt) REVERT: F 227 TYR cc_start: 0.8826 (t80) cc_final: 0.8161 (t80) REVERT: G 133 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7886 (mm-30) REVERT: G 241 TYR cc_start: 0.8362 (m-80) cc_final: 0.7985 (m-80) REVERT: G 258 MET cc_start: 0.7041 (mmm) cc_final: 0.6472 (tpt) REVERT: H 5 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7452 (tp) REVERT: H 24 ILE cc_start: 0.5110 (OUTLIER) cc_final: 0.4038 (tp) REVERT: H 258 MET cc_start: 0.8100 (mmm) cc_final: 0.7767 (mmm) REVERT: I 12 LYS cc_start: 0.8625 (tppt) cc_final: 0.8212 (tppt) outliers start: 71 outliers final: 51 residues processed: 465 average time/residue: 0.2605 time to fit residues: 179.0820 Evaluate side-chains 479 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 421 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 87 LEU 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 198 LEU 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 146 GLU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain D residue 74 MET 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 86 GLU 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 262 SER 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 213 PHE 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 132 GLU 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 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 150 ILE Chi-restraints excluded: chain J residue 190 GLN 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 125 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15928 Z= 0.248 Angle : 0.661 10.735 21533 Z= 0.341 Chirality : 0.039 0.198 2501 Planarity : 0.004 0.056 2845 Dihedral : 4.095 26.103 2312 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.84 % Allowed : 24.15 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.18), residues: 2123 helix: 2.42 (0.12), residues: 1803 sheet: None (None), residues: 0 loop : -2.16 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 199 HIS 0.002 0.001 HIS F 193 PHE 0.028 0.002 PHE I 213 TYR 0.021 0.002 TYR E 145 ARG 0.006 0.000 ARG D 114 *********************** 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 499 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 428 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6660 (tp30) REVERT: A 145 TYR cc_start: 0.8985 (t80) cc_final: 0.8627 (t80) REVERT: B 60 MET cc_start: 0.8725 (tpp) cc_final: 0.8321 (tpp) REVERT: B 116 ASN cc_start: 0.7115 (p0) cc_final: 0.6902 (p0) REVERT: B 146 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: C 40 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6553 (t80) REVERT: C 61 TYR cc_start: 0.8045 (t80) cc_final: 0.7805 (t80) REVERT: C 122 MET cc_start: 0.8038 (mmm) cc_final: 0.7808 (tpp) REVERT: C 146 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7054 (mm-30) REVERT: C 198 LEU cc_start: 0.9450 (tp) cc_final: 0.9216 (tp) REVERT: C 212 GLU cc_start: 0.8293 (tp30) cc_final: 0.8073 (tp30) REVERT: D 159 MET cc_start: 0.8693 (mmm) cc_final: 0.8068 (mmm) REVERT: E 44 LYS cc_start: 0.7274 (tppp) cc_final: 0.7035 (tppp) REVERT: E 45 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7299 (tp30) REVERT: E 53 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7248 (tm-30) REVERT: E 159 MET cc_start: 0.8015 (mmp) cc_final: 0.7556 (mmp) REVERT: F 86 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.6136 (tt0) REVERT: F 170 LYS cc_start: 0.9014 (mttt) cc_final: 0.8505 (tttt) REVERT: F 221 MET cc_start: 0.7879 (mmm) cc_final: 0.7655 (mmt) REVERT: F 227 TYR cc_start: 0.8831 (t80) cc_final: 0.8151 (t80) REVERT: G 133 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7816 (mm-30) REVERT: G 241 TYR cc_start: 0.8356 (m-80) cc_final: 0.7963 (m-80) REVERT: G 258 MET cc_start: 0.7008 (mmm) cc_final: 0.6459 (tpt) REVERT: H 5 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7441 (tp) REVERT: H 24 ILE cc_start: 0.4937 (OUTLIER) cc_final: 0.3882 (tp) REVERT: H 258 MET cc_start: 0.8150 (mmm) cc_final: 0.7834 (mmm) REVERT: I 12 LYS cc_start: 0.8599 (tppt) cc_final: 0.8176 (tppt) REVERT: J 265 SER cc_start: 0.8692 (p) cc_final: 0.8203 (t) outliers start: 71 outliers final: 52 residues processed: 464 average time/residue: 0.2623 time to fit residues: 179.6232 Evaluate side-chains 485 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 427 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 87 LEU 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 46 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 155 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 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 49 TRP 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 226 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 262 SER 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 153 LEU Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 213 PHE 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 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 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 190 GLN 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 193 optimal weight: 0.0060 chunk 176 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 170 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 197 GLN ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15928 Z= 0.228 Angle : 0.667 11.033 21533 Z= 0.340 Chirality : 0.039 0.212 2501 Planarity : 0.004 0.056 2845 Dihedral : 4.061 25.237 2312 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.02 % Allowed : 25.24 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.18), residues: 2123 helix: 2.46 (0.12), residues: 1803 sheet: None (None), residues: 0 loop : -2.11 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 199 HIS 0.001 0.001 HIS F 193 PHE 0.037 0.002 PHE I 213 TYR 0.021 0.002 TYR F 47 ARG 0.007 0.000 ARG D 114 *********************** 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 490 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 431 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6669 (tp30) REVERT: A 91 TYR cc_start: 0.7975 (m-80) cc_final: 0.7651 (m-80) REVERT: A 145 TYR cc_start: 0.8958 (t80) cc_final: 0.8609 (t80) REVERT: A 198 LEU cc_start: 0.9174 (tt) cc_final: 0.8863 (tp) REVERT: A 214 ASN cc_start: 0.8954 (t0) cc_final: 0.8727 (t0) REVERT: B 60 MET cc_start: 0.8740 (tpp) cc_final: 0.8339 (tpp) REVERT: B 146 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: C 40 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6551 (t80) REVERT: C 58 GLN cc_start: 0.7330 (mp10) cc_final: 0.7094 (mp10) REVERT: C 61 TYR cc_start: 0.8064 (t80) cc_final: 0.7821 (t80) REVERT: C 122 MET cc_start: 0.8003 (mmm) cc_final: 0.7768 (tpp) REVERT: C 146 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: C 212 GLU cc_start: 0.8291 (tp30) cc_final: 0.8077 (tp30) REVERT: D 124 ARG cc_start: 0.7275 (ptp90) cc_final: 0.6896 (ptp90) REVERT: D 145 TYR cc_start: 0.8478 (t80) cc_final: 0.8237 (t80) REVERT: D 159 MET cc_start: 0.8686 (mmm) cc_final: 0.8016 (mmt) REVERT: E 44 LYS cc_start: 0.7246 (tppp) cc_final: 0.7041 (tppp) REVERT: E 45 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7214 (tp30) REVERT: E 53 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7241 (tm-30) REVERT: E 159 MET cc_start: 0.7991 (mmp) cc_final: 0.7591 (mmp) REVERT: F 170 LYS cc_start: 0.9023 (mttt) cc_final: 0.8490 (tttt) REVERT: F 221 MET cc_start: 0.7868 (mmm) cc_final: 0.7638 (mmt) REVERT: F 227 TYR cc_start: 0.8837 (t80) cc_final: 0.8212 (t80) REVERT: G 133 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7811 (mm-30) REVERT: G 241 TYR cc_start: 0.8243 (m-80) cc_final: 0.7842 (m-80) REVERT: G 258 MET cc_start: 0.6974 (mmm) cc_final: 0.6488 (tpt) REVERT: H 5 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7457 (tp) REVERT: I 12 LYS cc_start: 0.8572 (tppt) cc_final: 0.8152 (tppt) REVERT: J 237 GLN cc_start: 0.8293 (pp30) cc_final: 0.7996 (pp30) REVERT: J 265 SER cc_start: 0.8700 (p) cc_final: 0.8222 (t) outliers start: 59 outliers final: 46 residues processed: 461 average time/residue: 0.2712 time to fit residues: 184.6507 Evaluate side-chains 478 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 428 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 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 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 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 146 GLU Chi-restraints excluded: chain C residue 155 ILE 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 227 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 49 TRP 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 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 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 22 THR Chi-restraints excluded: chain H residue 132 GLU 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 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 190 GLN 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 199 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 30.0000 chunk 192 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15928 Z= 0.242 Angle : 0.688 10.814 21533 Z= 0.350 Chirality : 0.039 0.229 2501 Planarity : 0.004 0.077 2845 Dihedral : 4.049 24.610 2312 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.23 % Allowed : 25.51 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.18), residues: 2123 helix: 2.44 (0.12), residues: 1803 sheet: None (None), residues: 0 loop : -2.09 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 189 HIS 0.001 0.000 HIS H 193 PHE 0.034 0.002 PHE I 213 TYR 0.020 0.002 TYR F 47 ARG 0.007 0.000 ARG G 232 ********************** 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 495 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 433 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6674 (tp30) REVERT: A 145 TYR cc_start: 0.8958 (t80) cc_final: 0.8599 (t80) REVERT: A 198 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8872 (tp) REVERT: A 214 ASN cc_start: 0.8948 (t0) cc_final: 0.8710 (t0) REVERT: B 60 MET cc_start: 0.8751 (tpp) cc_final: 0.8348 (tpp) REVERT: B 146 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: C 43 MET cc_start: 0.6897 (mtm) cc_final: 0.6651 (mtm) REVERT: C 58 GLN cc_start: 0.7327 (mp10) cc_final: 0.7099 (mp10) REVERT: C 61 TYR cc_start: 0.8062 (t80) cc_final: 0.7827 (t80) REVERT: C 122 MET cc_start: 0.7962 (mmm) cc_final: 0.7715 (tpp) REVERT: C 146 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: C 198 LEU cc_start: 0.9409 (tp) cc_final: 0.9045 (tp) REVERT: C 215 MET cc_start: 0.7897 (ttm) cc_final: 0.7484 (mtp) REVERT: D 145 TYR cc_start: 0.8501 (t80) cc_final: 0.8258 (t80) REVERT: D 159 MET cc_start: 0.8776 (mmm) cc_final: 0.8076 (mmt) REVERT: E 44 LYS cc_start: 0.7196 (tppp) cc_final: 0.6982 (tppp) REVERT: E 45 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7216 (tp30) REVERT: E 53 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7308 (tm-30) REVERT: E 159 MET cc_start: 0.8023 (mmp) cc_final: 0.7660 (mmp) REVERT: F 86 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5955 (tt0) REVERT: F 170 LYS cc_start: 0.9010 (mttt) cc_final: 0.8475 (tttt) REVERT: F 192 THR cc_start: 0.6809 (OUTLIER) cc_final: 0.6420 (p) REVERT: F 221 MET cc_start: 0.7857 (mmm) cc_final: 0.7602 (mmt) REVERT: F 227 TYR cc_start: 0.8845 (t80) cc_final: 0.8165 (t80) REVERT: G 133 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7820 (mm-30) REVERT: G 241 TYR cc_start: 0.8336 (m-80) cc_final: 0.7952 (m-80) REVERT: G 258 MET cc_start: 0.6942 (mmm) cc_final: 0.6688 (tpt) REVERT: H 5 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7539 (tp) REVERT: H 24 ILE cc_start: 0.5110 (OUTLIER) cc_final: 0.4595 (pt) REVERT: I 12 LYS cc_start: 0.8576 (tppt) cc_final: 0.8149 (tppt) REVERT: J 237 GLN cc_start: 0.8293 (pp30) cc_final: 0.8015 (pp30) REVERT: J 265 SER cc_start: 0.8712 (p) cc_final: 0.8257 (t) outliers start: 62 outliers final: 51 residues processed: 465 average time/residue: 0.2723 time to fit residues: 186.5142 Evaluate side-chains 482 residues out of total 1659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 424 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 73 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 198 LEU 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 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 146 GLU Chi-restraints excluded: chain C residue 155 ILE 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 138 LYS Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 49 TRP 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 226 SER Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 262 SER 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 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 132 GLU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 16 THR 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 190 GLN 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 177 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 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 = 0.4000 r_free = 0.4000 target = 0.163860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.152229 restraints weight = 25556.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.155082 restraints weight = 15349.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157077 restraints weight = 9253.689| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15928 Z= 0.218 Angle : 0.681 10.674 21533 Z= 0.343 Chirality : 0.039 0.277 2501 Planarity : 0.004 0.055 2845 Dihedral : 3.994 24.172 2312 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.75 % Allowed : 26.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.18), residues: 2123 helix: 2.51 (0.12), residues: 1803 sheet: None (None), residues: 0 loop : -2.00 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 189 HIS 0.001 0.000 HIS F 193 PHE 0.033 0.002 PHE G 213 TYR 0.021 0.002 TYR F 47 ARG 0.009 0.000 ARG D 124 =============================================================================== Job complete usr+sys time: 3504.91 seconds wall clock time: 62 minutes 58.37 seconds (3778.37 seconds total)