Starting phenix.real_space_refine on Thu Jun 19 14:48:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g2r_50981/06_2025/9g2r_50981.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g2r_50981/06_2025/9g2r_50981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g2r_50981/06_2025/9g2r_50981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g2r_50981/06_2025/9g2r_50981.map" model { file = "/net/cci-nas-00/data/ceres_data/9g2r_50981/06_2025/9g2r_50981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g2r_50981/06_2025/9g2r_50981.cif" } resolution = 3.88 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 96 5.16 5 C 14160 2.51 5 N 3988 2.21 5 O 4376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22620 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1817 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1817 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1817 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "D" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1817 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "E" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1939 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain: "F" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1899 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "G" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1939 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain: "H" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1899 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "I" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1939 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain: "J" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1899 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "K" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1939 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 6, 'TRANS': 235} Chain: "L" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1899 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Time building chain proxies: 12.97, per 1000 atoms: 0.57 Number of scatterers: 22620 At special positions: 0 Unit cell: (148.736, 147.408, 171.312, 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 96 16.00 O 4376 8.00 N 3988 7.00 C 14160 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: 5.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 93.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 11 through 31 removed outlier: 3.851A pdb=" N ALA A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 92 through 109 Processing helix chain 'A' and resid 112 through 143 Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.688A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 181 Processing helix chain 'A' and resid 184 through 252 removed outlier: 3.864A pdb=" N ILE A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 31 Processing helix chain 'B' and resid 39 through 68 Processing helix chain 'B' and resid 70 through 76 Processing helix chain 'B' and resid 92 through 109 Processing helix chain 'B' and resid 112 through 143 Processing helix chain 'B' and resid 143 through 153 Processing helix chain 'B' and resid 153 through 182 Processing helix chain 'B' and resid 184 through 252 removed outlier: 3.820A pdb=" N ILE B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 31 Processing helix chain 'C' and resid 39 through 68 Processing helix chain 'C' and resid 70 through 76 Processing helix chain 'C' and resid 92 through 109 Processing helix chain 'C' and resid 112 through 143 Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.688A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 181 Processing helix chain 'C' and resid 184 through 252 removed outlier: 3.864A pdb=" N ILE C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 31 Processing helix chain 'D' and resid 39 through 68 Processing helix chain 'D' and resid 70 through 76 Processing helix chain 'D' and resid 92 through 109 Processing helix chain 'D' and resid 112 through 143 Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 153 through 182 Processing helix chain 'D' and resid 184 through 252 removed outlier: 3.820A pdb=" N ILE D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 30 Processing helix chain 'E' and resid 39 through 68 Processing helix chain 'E' and resid 70 through 84 removed outlier: 3.578A pdb=" N ARG E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 109 Processing helix chain 'E' and resid 112 through 143 Processing helix chain 'E' and resid 143 through 181 removed outlier: 4.107A pdb=" N TYR E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 215 removed outlier: 3.972A pdb=" N GLY E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 252 removed outlier: 3.884A pdb=" N THR E 219 " --> pdb=" O GLY E 215 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 30 Processing helix chain 'F' and resid 39 through 68 Processing helix chain 'F' and resid 70 through 84 removed outlier: 3.520A pdb=" N ARG F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 109 Processing helix chain 'F' and resid 112 through 143 Processing helix chain 'F' and resid 143 through 153 removed outlier: 3.529A pdb=" N LEU F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 181 removed outlier: 3.541A pdb=" N THR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 215 Processing helix chain 'F' and resid 215 through 252 Processing helix chain 'G' and resid 12 through 30 Processing helix chain 'G' and resid 39 through 68 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.579A pdb=" N ARG G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 112 through 143 Processing helix chain 'G' and resid 143 through 181 removed outlier: 4.107A pdb=" N TYR G 155 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 215 removed outlier: 3.971A pdb=" N GLY G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 252 removed outlier: 3.884A pdb=" N THR G 219 " --> pdb=" O GLY G 215 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 30 Processing helix chain 'H' and resid 39 through 68 Processing helix chain 'H' and resid 70 through 84 removed outlier: 3.519A pdb=" N ARG H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 109 Processing helix chain 'H' and resid 112 through 143 Processing helix chain 'H' and resid 143 through 153 removed outlier: 3.529A pdb=" N LEU H 147 " --> pdb=" O PHE H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 181 removed outlier: 3.541A pdb=" N THR H 157 " --> pdb=" O GLY H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 215 Processing helix chain 'H' and resid 215 through 252 Processing helix chain 'I' and resid 12 through 30 Processing helix chain 'I' and resid 39 through 68 Processing helix chain 'I' and resid 70 through 83 removed outlier: 3.579A pdb=" N ARG I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 109 Processing helix chain 'I' and resid 112 through 143 Processing helix chain 'I' and resid 143 through 181 removed outlier: 4.107A pdb=" N TYR I 155 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS I 156 " --> pdb=" O GLU I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 215 removed outlier: 3.972A pdb=" N GLY I 215 " --> pdb=" O LEU I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 252 removed outlier: 3.884A pdb=" N THR I 219 " --> pdb=" O GLY I 215 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS I 220 " --> pdb=" O ILE I 216 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA I 221 " --> pdb=" O SER I 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 30 Processing helix chain 'J' and resid 39 through 68 Processing helix chain 'J' and resid 70 through 84 removed outlier: 3.520A pdb=" N ARG J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 109 Processing helix chain 'J' and resid 112 through 143 Processing helix chain 'J' and resid 143 through 153 removed outlier: 3.529A pdb=" N LEU J 147 " --> pdb=" O PHE J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 181 removed outlier: 3.541A pdb=" N THR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 215 Processing helix chain 'J' and resid 215 through 252 Processing helix chain 'K' and resid 12 through 30 Processing helix chain 'K' and resid 39 through 68 Processing helix chain 'K' and resid 70 through 84 removed outlier: 3.579A pdb=" N ARG K 74 " --> pdb=" O ASN K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 109 Processing helix chain 'K' and resid 112 through 143 Processing helix chain 'K' and resid 143 through 181 removed outlier: 4.107A pdb=" N TYR K 155 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 215 removed outlier: 3.971A pdb=" N GLY K 215 " --> pdb=" O LEU K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 252 removed outlier: 3.884A pdb=" N THR K 219 " --> pdb=" O GLY K 215 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS K 220 " --> pdb=" O ILE K 216 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA K 221 " --> pdb=" O SER K 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 30 Processing helix chain 'L' and resid 39 through 68 Processing helix chain 'L' and resid 70 through 84 removed outlier: 3.520A pdb=" N ARG L 74 " --> pdb=" O ASN L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 109 Processing helix chain 'L' and resid 112 through 143 Processing helix chain 'L' and resid 143 through 153 removed outlier: 3.528A pdb=" N LEU L 147 " --> pdb=" O PHE L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 181 removed outlier: 3.541A pdb=" N THR L 157 " --> pdb=" O GLY L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 215 Processing helix chain 'L' and resid 215 through 252 2185 hydrogen bonds defined for protein. 6555 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: 9.91 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4925 1.33 - 1.45: 4571 1.45 - 1.57: 13284 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 22924 Sorted by residual: bond pdb=" N THR C 145 " pdb=" CA THR C 145 " ideal model delta sigma weight residual 1.462 1.489 -0.027 7.70e-03 1.69e+04 1.24e+01 bond pdb=" N THR A 145 " pdb=" CA THR A 145 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.15e+01 bond pdb=" N ILE K 91 " pdb=" CA ILE K 91 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.20e-02 6.94e+03 8.62e+00 bond pdb=" N ASN D 93 " pdb=" CA ASN D 93 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.54e+00 bond pdb=" N ASN B 93 " pdb=" CA ASN B 93 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.53e+00 ... (remaining 22919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 21067 1.05 - 2.10: 5003 2.10 - 3.15: 4529 3.15 - 4.20: 197 4.20 - 5.25: 48 Bond angle restraints: 30844 Sorted by residual: angle pdb=" N LEU G 30 " pdb=" CA LEU G 30 " pdb=" C LEU G 30 " ideal model delta sigma weight residual 112.87 108.06 4.81 1.20e+00 6.94e-01 1.61e+01 angle pdb=" N LEU I 30 " pdb=" CA LEU I 30 " pdb=" C LEU I 30 " ideal model delta sigma weight residual 112.87 108.07 4.80 1.20e+00 6.94e-01 1.60e+01 angle pdb=" N LEU K 30 " pdb=" CA LEU K 30 " pdb=" C LEU K 30 " ideal model delta sigma weight residual 112.87 108.08 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" N LEU E 30 " pdb=" CA LEU E 30 " pdb=" C LEU E 30 " ideal model delta sigma weight residual 112.87 108.08 4.79 1.20e+00 6.94e-01 1.59e+01 angle pdb=" N GLY G 31 " pdb=" CA GLY G 31 " pdb=" C GLY G 31 " ideal model delta sigma weight residual 115.40 110.26 5.14 1.32e+00 5.74e-01 1.52e+01 ... (remaining 30839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 12861 15.51 - 31.01: 961 31.01 - 46.52: 223 46.52 - 62.02: 165 62.02 - 77.53: 30 Dihedral angle restraints: 14240 sinusoidal: 5952 harmonic: 8288 Sorted by residual: dihedral pdb=" CD ARG H 210 " pdb=" NE ARG H 210 " pdb=" CZ ARG H 210 " pdb=" NH1 ARG H 210 " ideal model delta sinusoidal sigma weight residual 0.00 32.72 -32.72 1 1.00e+01 1.00e-02 1.52e+01 dihedral pdb=" CD ARG L 210 " pdb=" NE ARG L 210 " pdb=" CZ ARG L 210 " pdb=" NH1 ARG L 210 " ideal model delta sinusoidal sigma weight residual 0.00 32.61 -32.61 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CD ARG F 210 " pdb=" NE ARG F 210 " pdb=" CZ ARG F 210 " pdb=" NH1 ARG F 210 " ideal model delta sinusoidal sigma weight residual 0.00 32.61 -32.61 1 1.00e+01 1.00e-02 1.51e+01 ... (remaining 14237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1344 0.044 - 0.088: 779 0.088 - 0.132: 813 0.132 - 0.176: 440 0.176 - 0.220: 112 Chirality restraints: 3488 Sorted by residual: chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE A 208 " pdb=" N ILE A 208 " pdb=" C ILE A 208 " pdb=" CB ILE A 208 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3485 not shown) Planarity restraints: 4012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 210 " -0.574 9.50e-02 1.11e+02 2.57e-01 4.05e+01 pdb=" NE ARG H 210 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG H 210 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG H 210 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 210 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 210 " 0.574 9.50e-02 1.11e+02 2.57e-01 4.05e+01 pdb=" NE ARG L 210 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG L 210 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG L 210 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 210 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 210 " -0.574 9.50e-02 1.11e+02 2.57e-01 4.04e+01 pdb=" NE ARG F 210 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG F 210 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 210 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 210 " -0.017 2.00e-02 2.50e+03 ... (remaining 4009 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8339 2.86 - 3.37: 26375 3.37 - 3.88: 39049 3.88 - 4.39: 44756 4.39 - 4.90: 67443 Nonbonded interactions: 185962 Sorted by model distance: nonbonded pdb=" O SER J 200 " pdb=" OD1 ASP J 203 " model vdw 2.353 3.040 nonbonded pdb=" O SER F 200 " pdb=" OD1 ASP F 203 " model vdw 2.354 3.040 nonbonded pdb=" O SER H 200 " pdb=" OD1 ASP H 203 " model vdw 2.354 3.040 nonbonded pdb=" O SER L 200 " pdb=" OD1 ASP L 203 " model vdw 2.354 3.040 nonbonded pdb=" NE2 GLN K 243 " pdb=" OD1 ASP K 247 " model vdw 2.399 3.120 ... (remaining 185957 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 30 or resid 35 through 252)) selection = (chain 'B' and (resid 13 through 30 or resid 35 through 252)) selection = (chain 'C' and (resid 13 through 30 or resid 35 through 252)) selection = (chain 'D' and (resid 13 through 30 or resid 35 through 252)) selection = (chain 'E' and (resid 13 through 30 or resid 35 through 76 or resid 91 through 2 \ 52)) selection = (chain 'F' and (resid 13 through 76 or resid 91 through 252)) selection = (chain 'G' and (resid 13 through 30 or resid 35 through 76 or resid 91 through 2 \ 52)) selection = (chain 'H' and (resid 13 through 76 or resid 91 through 252)) selection = (chain 'I' and (resid 13 through 30 or resid 35 through 76 or resid 91 through 2 \ 52)) selection = (chain 'J' and (resid 13 through 76 or resid 91 through 252)) selection = (chain 'K' and (resid 13 through 30 or resid 35 through 76 or resid 91 through 2 \ 52)) selection = (chain 'L' and (resid 13 through 76 or resid 91 through 252)) } 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: 1.210 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: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 50.650 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.100 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:3.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.010 0.045 22924 Z= 0.755 Angle : 1.235 5.251 30844 Z= 1.038 Chirality : 0.090 0.220 3488 Planarity : 0.023 0.257 4012 Dihedral : 13.902 77.527 8848 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.58 % Allowed : 4.01 % Favored : 95.41 % 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: 0.17 (0.14), residues: 2784 helix: 0.42 (0.09), residues: 2548 sheet: None (None), residues: 0 loop : -2.11 (0.31), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 55 HIS 0.007 0.001 HIS J 41 PHE 0.028 0.002 PHE L 78 TYR 0.024 0.002 TYR K 244 ARG 0.036 0.003 ARG E 127 Details of bonding type rmsd hydrogen bonds : bond 0.16674 ( 2185) hydrogen bonds : angle 6.37205 ( 6555) covalent geometry : bond 0.00967 (22924) covalent geometry : angle 1.23505 (30844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 250 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8777 (ppp) REVERT: H 101 MET cc_start: 0.8822 (mtt) cc_final: 0.8449 (mtm) REVERT: H 237 TYR cc_start: 0.8162 (t80) cc_final: 0.7815 (t80) REVERT: I 132 ASP cc_start: 0.8108 (t0) cc_final: 0.7508 (t0) outliers start: 14 outliers final: 1 residues processed: 260 average time/residue: 0.4702 time to fit residues: 191.4218 Evaluate side-chains 106 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain L residue 60 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 166 GLN A 234 GLN B 41 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 41 HIS K 220 HIS ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 249 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.061217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.047198 restraints weight = 197687.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.046715 restraints weight = 95278.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.046860 restraints weight = 75425.113| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22924 Z= 0.174 Angle : 0.578 10.794 30844 Z= 0.308 Chirality : 0.036 0.366 3488 Planarity : 0.004 0.031 4012 Dihedral : 2.984 16.064 3074 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.03 % Allowed : 6.78 % Favored : 92.19 % 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: 4.55 (0.14), residues: 2784 helix: 3.22 (0.09), residues: 2584 sheet: None (None), residues: 0 loop : -0.70 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 55 HIS 0.006 0.001 HIS G 41 PHE 0.022 0.002 PHE J 230 TYR 0.024 0.002 TYR I 155 ARG 0.006 0.001 ARG A 162 Details of bonding type rmsd hydrogen bonds : bond 0.06990 ( 2185) hydrogen bonds : angle 4.01920 ( 6555) covalent geometry : bond 0.00330 (22924) covalent geometry : angle 0.57751 (30844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 60 MET cc_start: 0.7764 (tmm) cc_final: 0.7485 (ttm) REVERT: C 179 LEU cc_start: 0.9237 (tp) cc_final: 0.8793 (pp) REVERT: C 229 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8279 (t0) REVERT: E 227 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9056 (pp) REVERT: G 60 MET cc_start: 0.8836 (tpp) cc_final: 0.8559 (tpp) REVERT: H 237 TYR cc_start: 0.8268 (t80) cc_final: 0.8031 (t80) REVERT: I 235 MET cc_start: 0.9367 (tpp) cc_final: 0.9030 (tpp) REVERT: J 60 MET cc_start: 0.9505 (mmm) cc_final: 0.9165 (mmm) REVERT: J 143 PHE cc_start: 0.8886 (t80) cc_final: 0.8659 (t80) REVERT: K 100 TYR cc_start: 0.9152 (m-10) cc_final: 0.8945 (m-10) outliers start: 25 outliers final: 9 residues processed: 132 average time/residue: 0.4289 time to fit residues: 94.5299 Evaluate side-chains 99 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 3.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain L residue 83 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 141 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 88 optimal weight: 30.0000 chunk 169 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 228 ASN E 222 HIS E 251 GLN F 116 ASN H 116 ASN H 243 GLN I 249 GLN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.059433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.045639 restraints weight = 200110.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.044750 restraints weight = 107248.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.044901 restraints weight = 89676.797| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22924 Z= 0.165 Angle : 0.543 12.251 30844 Z= 0.283 Chirality : 0.033 0.198 3488 Planarity : 0.004 0.042 4012 Dihedral : 3.064 17.727 3068 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.28 % Allowed : 7.98 % Favored : 90.74 % 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: 5.33 (0.14), residues: 2784 helix: 3.74 (0.09), residues: 2576 sheet: None (None), residues: 0 loop : -0.62 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 55 HIS 0.005 0.001 HIS G 41 PHE 0.021 0.002 PHE I 230 TYR 0.029 0.002 TYR L 238 ARG 0.005 0.001 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.05966 ( 2185) hydrogen bonds : angle 3.65108 ( 6555) covalent geometry : bond 0.00321 (22924) covalent geometry : angle 0.54334 (30844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.8461 (ttp) cc_final: 0.8098 (ttt) REVERT: B 235 MET cc_start: 0.8403 (tmm) cc_final: 0.8171 (tmm) REVERT: C 60 MET cc_start: 0.7777 (tmm) cc_final: 0.7546 (ttm) REVERT: C 179 LEU cc_start: 0.9320 (tp) cc_final: 0.8896 (pp) REVERT: D 19 LEU cc_start: 0.9651 (mt) cc_final: 0.9433 (pp) REVERT: E 101 MET cc_start: 0.8851 (ptp) cc_final: 0.8623 (ptp) REVERT: G 60 MET cc_start: 0.8774 (tpp) cc_final: 0.8423 (tpp) REVERT: H 237 TYR cc_start: 0.8190 (t80) cc_final: 0.7813 (t80) REVERT: I 235 MET cc_start: 0.9303 (tpp) cc_final: 0.8786 (tpp) REVERT: J 238 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8942 (m-10) REVERT: K 237 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8561 (t80) REVERT: L 60 MET cc_start: 0.9441 (ptt) cc_final: 0.9180 (ppp) outliers start: 31 outliers final: 21 residues processed: 120 average time/residue: 0.3085 time to fit residues: 61.9633 Evaluate side-chains 107 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain J residue 238 TYR Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 245 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 54 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS G 222 HIS ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 HIS J 116 ASN K 228 ASN ** K 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.057508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.040803 restraints weight = 205552.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.041702 restraints weight = 106997.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.041985 restraints weight = 55048.926| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22924 Z= 0.211 Angle : 0.594 9.571 30844 Z= 0.316 Chirality : 0.035 0.162 3488 Planarity : 0.004 0.037 4012 Dihedral : 3.285 18.254 3068 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.53 % Allowed : 9.01 % Favored : 89.46 % 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: 4.84 (0.14), residues: 2784 helix: 3.41 (0.09), residues: 2576 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 55 HIS 0.006 0.001 HIS I 41 PHE 0.027 0.002 PHE I 230 TYR 0.029 0.002 TYR B 238 ARG 0.006 0.001 ARG E 225 Details of bonding type rmsd hydrogen bonds : bond 0.06119 ( 2185) hydrogen bonds : angle 3.81567 ( 6555) covalent geometry : bond 0.00441 (22924) covalent geometry : angle 0.59430 (30844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8497 (tmm) cc_final: 0.8097 (tmm) REVERT: B 235 MET cc_start: 0.8438 (tmm) cc_final: 0.8008 (tmm) REVERT: C 179 LEU cc_start: 0.9419 (tp) cc_final: 0.8991 (pp) REVERT: D 120 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8789 (mmtm) REVERT: E 245 MET cc_start: 0.8989 (ttm) cc_final: 0.8334 (ttt) REVERT: F 235 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8015 (mmt) REVERT: G 60 MET cc_start: 0.9035 (tpp) cc_final: 0.8728 (tpp) REVERT: G 101 MET cc_start: 0.8652 (ptt) cc_final: 0.8284 (ptt) REVERT: G 245 MET cc_start: 0.9213 (ttm) cc_final: 0.8904 (ttm) REVERT: H 237 TYR cc_start: 0.8508 (t80) cc_final: 0.8061 (t80) REVERT: J 60 MET cc_start: 0.9590 (mmm) cc_final: 0.9111 (mmm) REVERT: J 245 MET cc_start: 0.8967 (tpt) cc_final: 0.8623 (tpp) REVERT: K 143 PHE cc_start: 0.9578 (t80) cc_final: 0.9302 (m-80) REVERT: K 237 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8769 (t80) REVERT: L 60 MET cc_start: 0.9453 (ptt) cc_final: 0.9198 (ptt) outliers start: 37 outliers final: 30 residues processed: 115 average time/residue: 0.3078 time to fit residues: 59.7496 Evaluate side-chains 112 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain J residue 237 TYR Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 242 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 83 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 29 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 223 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN D 41 HIS D 99 GLN E 228 ASN ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.058025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.041694 restraints weight = 203099.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.042496 restraints weight = 103855.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.042591 restraints weight = 58441.922| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22924 Z= 0.139 Angle : 0.500 12.709 30844 Z= 0.258 Chirality : 0.032 0.160 3488 Planarity : 0.003 0.043 4012 Dihedral : 3.105 16.812 3068 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.45 % Allowed : 9.83 % Favored : 88.72 % 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: 5.51 (0.14), residues: 2784 helix: 3.87 (0.09), residues: 2564 sheet: None (None), residues: 0 loop : -0.44 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 55 HIS 0.005 0.001 HIS I 41 PHE 0.021 0.001 PHE J 230 TYR 0.029 0.001 TYR L 238 ARG 0.003 0.001 ARG L 178 Details of bonding type rmsd hydrogen bonds : bond 0.05395 ( 2185) hydrogen bonds : angle 3.43852 ( 6555) covalent geometry : bond 0.00271 (22924) covalent geometry : angle 0.49992 (30844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8527 (tmm) cc_final: 0.8108 (tmm) REVERT: A 245 MET cc_start: 0.8412 (tpp) cc_final: 0.8203 (ttm) REVERT: C 60 MET cc_start: 0.8097 (ttp) cc_final: 0.7082 (tmm) REVERT: C 179 LEU cc_start: 0.9363 (tp) cc_final: 0.8958 (pp) REVERT: E 235 MET cc_start: 0.9096 (tpp) cc_final: 0.8864 (tpp) REVERT: E 245 MET cc_start: 0.8869 (ttm) cc_final: 0.8585 (ttm) REVERT: G 60 MET cc_start: 0.9057 (tpp) cc_final: 0.8740 (tpp) REVERT: G 101 MET cc_start: 0.8707 (ptt) cc_final: 0.8501 (ptt) REVERT: H 237 TYR cc_start: 0.8327 (t80) cc_final: 0.8042 (t80) REVERT: H 245 MET cc_start: 0.9357 (tpp) cc_final: 0.8877 (ttm) REVERT: I 245 MET cc_start: 0.9587 (ttm) cc_final: 0.9275 (ttt) REVERT: J 60 MET cc_start: 0.9601 (mmm) cc_final: 0.9133 (mmm) REVERT: J 245 MET cc_start: 0.8874 (tpt) cc_final: 0.8519 (tpp) REVERT: K 143 PHE cc_start: 0.9539 (t80) cc_final: 0.9249 (m-80) REVERT: K 237 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8596 (t80) REVERT: L 60 MET cc_start: 0.9449 (ptt) cc_final: 0.9194 (ptt) outliers start: 35 outliers final: 23 residues processed: 108 average time/residue: 0.3187 time to fit residues: 57.4236 Evaluate side-chains 102 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 242 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 188 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 96 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 182 optimal weight: 50.0000 chunk 159 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 228 ASN I 243 GLN ** K 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.057572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.041316 restraints weight = 201577.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.042006 restraints weight = 112288.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.042007 restraints weight = 62024.590| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22924 Z= 0.149 Angle : 0.525 10.493 30844 Z= 0.269 Chirality : 0.032 0.176 3488 Planarity : 0.003 0.040 4012 Dihedral : 3.115 17.344 3068 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.90 % Allowed : 10.25 % Favored : 87.85 % 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: 5.49 (0.14), residues: 2784 helix: 3.84 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 55 HIS 0.005 0.001 HIS I 41 PHE 0.021 0.001 PHE J 230 TYR 0.027 0.002 TYR L 238 ARG 0.010 0.001 ARG H 178 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 2185) hydrogen bonds : angle 3.44793 ( 6555) covalent geometry : bond 0.00301 (22924) covalent geometry : angle 0.52523 (30844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 78 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8554 (tmm) cc_final: 0.8123 (tmm) REVERT: C 60 MET cc_start: 0.8175 (ttp) cc_final: 0.7082 (tmm) REVERT: C 179 LEU cc_start: 0.9334 (tp) cc_final: 0.8913 (pp) REVERT: D 60 MET cc_start: 0.8002 (ttt) cc_final: 0.7553 (tmm) REVERT: D 120 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8823 (mmtm) REVERT: E 235 MET cc_start: 0.9290 (tpp) cc_final: 0.9003 (tpp) REVERT: E 245 MET cc_start: 0.8848 (ttm) cc_final: 0.8632 (ttm) REVERT: F 245 MET cc_start: 0.8339 (ttm) cc_final: 0.8058 (ttm) REVERT: G 60 MET cc_start: 0.9069 (tpp) cc_final: 0.8772 (tpp) REVERT: G 245 MET cc_start: 0.9114 (ttm) cc_final: 0.8742 (ttm) REVERT: H 237 TYR cc_start: 0.8314 (t80) cc_final: 0.8034 (t80) REVERT: H 245 MET cc_start: 0.9354 (tpp) cc_final: 0.9112 (ttm) REVERT: I 230 PHE cc_start: 0.9670 (t80) cc_final: 0.9469 (t80) REVERT: I 245 MET cc_start: 0.9572 (ttm) cc_final: 0.9230 (ttp) REVERT: J 60 MET cc_start: 0.9610 (mmm) cc_final: 0.9128 (mmm) REVERT: J 245 MET cc_start: 0.9065 (tpt) cc_final: 0.8733 (tpp) REVERT: K 143 PHE cc_start: 0.9574 (t80) cc_final: 0.9276 (m-80) REVERT: K 237 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8830 (t80) REVERT: L 60 MET cc_start: 0.9461 (ptt) cc_final: 0.9144 (ptm) REVERT: L 245 MET cc_start: 0.5675 (ppp) cc_final: 0.5360 (ptm) outliers start: 46 outliers final: 29 residues processed: 118 average time/residue: 0.3164 time to fit residues: 62.0950 Evaluate side-chains 106 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 234 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 22 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.058582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.045172 restraints weight = 203954.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.044200 restraints weight = 108313.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.044358 restraints weight = 90024.058| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22924 Z= 0.119 Angle : 0.500 11.453 30844 Z= 0.250 Chirality : 0.032 0.361 3488 Planarity : 0.003 0.039 4012 Dihedral : 3.023 17.593 3068 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.91 % Allowed : 10.99 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.99 (0.14), residues: 2784 helix: 4.17 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 55 HIS 0.005 0.001 HIS I 41 PHE 0.034 0.001 PHE I 143 TYR 0.023 0.001 TYR L 238 ARG 0.003 0.000 ARG L 178 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 2185) hydrogen bonds : angle 3.17432 ( 6555) covalent geometry : bond 0.00212 (22924) covalent geometry : angle 0.49958 (30844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8331 (tmm) cc_final: 0.7767 (tmm) REVERT: A 247 ASP cc_start: 0.9061 (m-30) cc_final: 0.8648 (t70) REVERT: C 60 MET cc_start: 0.7954 (ttp) cc_final: 0.6940 (tmm) REVERT: C 179 LEU cc_start: 0.9260 (tp) cc_final: 0.8836 (pp) REVERT: E 235 MET cc_start: 0.9114 (tpp) cc_final: 0.8909 (tpp) REVERT: F 245 MET cc_start: 0.8226 (ttm) cc_final: 0.7984 (ttm) REVERT: G 60 MET cc_start: 0.8899 (tpp) cc_final: 0.8635 (tpp) REVERT: G 245 MET cc_start: 0.8935 (ttm) cc_final: 0.8354 (ttm) REVERT: H 101 MET cc_start: 0.8676 (ttp) cc_final: 0.8272 (ppp) REVERT: H 237 TYR cc_start: 0.8192 (t80) cc_final: 0.7964 (t80) REVERT: H 245 MET cc_start: 0.9197 (tpp) cc_final: 0.8897 (ttm) REVERT: I 230 PHE cc_start: 0.9493 (t80) cc_final: 0.9278 (t80) REVERT: I 245 MET cc_start: 0.9528 (ttm) cc_final: 0.9161 (ttt) REVERT: J 60 MET cc_start: 0.9582 (mmm) cc_final: 0.9106 (mmm) REVERT: J 114 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: J 235 MET cc_start: 0.9269 (ppp) cc_final: 0.8968 (ppp) REVERT: J 245 MET cc_start: 0.9047 (tpt) cc_final: 0.8737 (tpp) REVERT: K 143 PHE cc_start: 0.9513 (t80) cc_final: 0.9203 (m-80) REVERT: K 237 TYR cc_start: 0.9093 (OUTLIER) cc_final: 0.8625 (t80) REVERT: L 60 MET cc_start: 0.9428 (ptt) cc_final: 0.9158 (ptm) REVERT: L 245 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5517 (ptm) outliers start: 22 outliers final: 17 residues processed: 106 average time/residue: 0.3035 time to fit residues: 54.1474 Evaluate side-chains 96 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 114 TYR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 242 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 245 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 59 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 104 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS F 249 GLN ** K 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.056986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.043790 restraints weight = 203275.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.042546 restraints weight = 114109.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.042681 restraints weight = 93795.446| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22924 Z= 0.189 Angle : 0.592 12.496 30844 Z= 0.303 Chirality : 0.034 0.258 3488 Planarity : 0.003 0.037 4012 Dihedral : 3.135 19.233 3068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.40 % Allowed : 10.87 % Favored : 87.73 % 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: 5.38 (0.14), residues: 2784 helix: 3.77 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 55 HIS 0.009 0.001 HIS K 41 PHE 0.039 0.002 PHE J 143 TYR 0.034 0.002 TYR L 238 ARG 0.006 0.001 ARG E 225 Details of bonding type rmsd hydrogen bonds : bond 0.05330 ( 2185) hydrogen bonds : angle 3.54492 ( 6555) covalent geometry : bond 0.00395 (22924) covalent geometry : angle 0.59180 (30844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8308 (tmm) cc_final: 0.8107 (tmm) REVERT: C 179 LEU cc_start: 0.9309 (tp) cc_final: 0.8874 (pp) REVERT: E 235 MET cc_start: 0.9112 (tpp) cc_final: 0.8721 (tpp) REVERT: E 245 MET cc_start: 0.8220 (ttt) cc_final: 0.7990 (ttt) REVERT: F 245 MET cc_start: 0.8663 (ttm) cc_final: 0.8199 (ttm) REVERT: G 60 MET cc_start: 0.8865 (tpp) cc_final: 0.8497 (tpp) REVERT: G 245 MET cc_start: 0.9202 (ttm) cc_final: 0.8793 (ttm) REVERT: H 101 MET cc_start: 0.8742 (ttp) cc_final: 0.8423 (ppp) REVERT: I 245 MET cc_start: 0.9540 (ttm) cc_final: 0.9317 (ttm) REVERT: J 60 MET cc_start: 0.9615 (mmm) cc_final: 0.9126 (mmm) REVERT: J 114 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: J 245 MET cc_start: 0.9008 (tpt) cc_final: 0.8560 (tpp) REVERT: K 97 LEU cc_start: 0.9628 (tp) cc_final: 0.9128 (mt) REVERT: K 100 TYR cc_start: 0.9220 (m-10) cc_final: 0.9016 (m-10) REVERT: K 143 PHE cc_start: 0.9535 (t80) cc_final: 0.9256 (m-80) REVERT: L 60 MET cc_start: 0.9435 (ptt) cc_final: 0.9158 (ptm) outliers start: 34 outliers final: 24 residues processed: 106 average time/residue: 0.3073 time to fit residues: 54.6094 Evaluate side-chains 97 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 114 TYR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 242 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 188 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 153 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 229 optimal weight: 50.0000 chunk 185 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS I 249 GLN K 41 HIS K 243 GLN ** L 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.057572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.041454 restraints weight = 202045.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.041613 restraints weight = 109070.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.042542 restraints weight = 63924.097| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22924 Z= 0.133 Angle : 0.536 11.986 30844 Z= 0.270 Chirality : 0.033 0.252 3488 Planarity : 0.003 0.036 4012 Dihedral : 3.101 19.294 3068 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.16 % Allowed : 11.40 % Favored : 87.44 % 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: 5.68 (0.15), residues: 2784 helix: 3.97 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 55 HIS 0.005 0.001 HIS I 41 PHE 0.039 0.001 PHE I 230 TYR 0.031 0.001 TYR L 238 ARG 0.003 0.000 ARG L 178 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 2185) hydrogen bonds : angle 3.35212 ( 6555) covalent geometry : bond 0.00264 (22924) covalent geometry : angle 0.53568 (30844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8524 (tmm) cc_final: 0.8045 (tmm) REVERT: A 247 ASP cc_start: 0.8871 (m-30) cc_final: 0.8613 (t70) REVERT: C 60 MET cc_start: 0.8058 (ttp) cc_final: 0.7051 (tmm) REVERT: C 179 LEU cc_start: 0.9295 (tp) cc_final: 0.8869 (pp) REVERT: E 101 MET cc_start: 0.9001 (ptp) cc_final: 0.8771 (ptp) REVERT: E 235 MET cc_start: 0.9296 (tpp) cc_final: 0.8708 (tpp) REVERT: E 245 MET cc_start: 0.8411 (ttt) cc_final: 0.7997 (ttt) REVERT: F 245 MET cc_start: 0.8525 (ttm) cc_final: 0.8117 (ttm) REVERT: G 60 MET cc_start: 0.9046 (tpp) cc_final: 0.8674 (tpp) REVERT: G 245 MET cc_start: 0.9053 (ttm) cc_final: 0.8491 (ttm) REVERT: H 101 MET cc_start: 0.8978 (ttp) cc_final: 0.8561 (ppp) REVERT: H 237 TYR cc_start: 0.8322 (t80) cc_final: 0.8086 (t80) REVERT: I 245 MET cc_start: 0.9584 (ttm) cc_final: 0.9283 (ttm) REVERT: J 60 MET cc_start: 0.9611 (mmm) cc_final: 0.9088 (mmm) REVERT: J 114 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: J 245 MET cc_start: 0.8988 (tpt) cc_final: 0.8524 (tpp) REVERT: K 97 LEU cc_start: 0.9610 (tp) cc_final: 0.9114 (mt) REVERT: K 100 TYR cc_start: 0.9331 (m-10) cc_final: 0.9122 (m-10) REVERT: K 143 PHE cc_start: 0.9604 (t80) cc_final: 0.9328 (m-80) REVERT: K 237 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8510 (t80) REVERT: L 60 MET cc_start: 0.9458 (ptt) cc_final: 0.9181 (ptm) REVERT: L 245 MET cc_start: 0.5654 (ptm) cc_final: 0.5197 (ptm) outliers start: 28 outliers final: 21 residues processed: 103 average time/residue: 0.3282 time to fit residues: 57.0480 Evaluate side-chains 97 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain J residue 114 TYR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 242 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 188 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 182 optimal weight: 50.0000 chunk 272 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS G 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.056693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.041305 restraints weight = 203992.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.040845 restraints weight = 126552.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.041049 restraints weight = 78647.734| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22924 Z= 0.174 Angle : 0.589 11.300 30844 Z= 0.303 Chirality : 0.034 0.232 3488 Planarity : 0.003 0.034 4012 Dihedral : 3.201 18.029 3068 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.20 % Allowed : 11.36 % Favored : 87.44 % 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: 5.29 (0.15), residues: 2784 helix: 3.71 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.37 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 55 HIS 0.006 0.001 HIS G 223 PHE 0.030 0.002 PHE J 143 TYR 0.039 0.002 TYR L 100 ARG 0.005 0.001 ARG E 225 Details of bonding type rmsd hydrogen bonds : bond 0.05269 ( 2185) hydrogen bonds : angle 3.55229 ( 6555) covalent geometry : bond 0.00363 (22924) covalent geometry : angle 0.58909 (30844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8609 (ttm) cc_final: 0.8154 (ttm) REVERT: E 101 MET cc_start: 0.9043 (ptp) cc_final: 0.8642 (ptp) REVERT: E 235 MET cc_start: 0.9260 (tpp) cc_final: 0.8873 (tpp) REVERT: E 245 MET cc_start: 0.8422 (ttt) cc_final: 0.8145 (ttt) REVERT: G 60 MET cc_start: 0.8989 (tpp) cc_final: 0.8628 (tpp) REVERT: H 101 MET cc_start: 0.8980 (ttp) cc_final: 0.8606 (ppp) REVERT: H 235 MET cc_start: 0.8789 (tmm) cc_final: 0.8497 (tmm) REVERT: I 245 MET cc_start: 0.9519 (ttm) cc_final: 0.9202 (ttm) REVERT: J 60 MET cc_start: 0.9573 (mmm) cc_final: 0.8977 (mmm) REVERT: J 114 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: J 245 MET cc_start: 0.9007 (tpt) cc_final: 0.8548 (tpp) REVERT: K 97 LEU cc_start: 0.9632 (tp) cc_final: 0.9115 (mt) REVERT: K 100 TYR cc_start: 0.9271 (m-10) cc_final: 0.9048 (m-10) REVERT: K 143 PHE cc_start: 0.9576 (t80) cc_final: 0.9314 (m-80) REVERT: K 237 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8622 (t80) REVERT: L 60 MET cc_start: 0.9443 (ptt) cc_final: 0.9192 (ptm) REVERT: L 245 MET cc_start: 0.5909 (ptm) cc_final: 0.5466 (ptm) outliers start: 29 outliers final: 24 residues processed: 96 average time/residue: 0.3185 time to fit residues: 51.2549 Evaluate side-chains 95 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 114 TYR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain K residue 242 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 188 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 112 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 229 optimal weight: 40.0000 chunk 185 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 237 optimal weight: 0.1980 chunk 246 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 182 optimal weight: 50.0000 chunk 8 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 222 HIS J 243 GLN ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.056052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.040667 restraints weight = 203267.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.040472 restraints weight = 129413.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.040475 restraints weight = 83445.203| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22924 Z= 0.198 Angle : 0.627 16.192 30844 Z= 0.324 Chirality : 0.035 0.279 3488 Planarity : 0.003 0.033 4012 Dihedral : 3.382 18.196 3068 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.20 % Allowed : 11.65 % Favored : 87.15 % 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: 4.78 (0.15), residues: 2784 helix: 3.37 (0.09), residues: 2580 sheet: None (None), residues: 0 loop : -0.50 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 55 HIS 0.008 0.001 HIS K 41 PHE 0.028 0.002 PHE J 230 TYR 0.032 0.002 TYR L 100 ARG 0.005 0.001 ARG E 225 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 2185) hydrogen bonds : angle 3.74590 ( 6555) covalent geometry : bond 0.00416 (22924) covalent geometry : angle 0.62709 (30844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7696.13 seconds wall clock time: 137 minutes 37.12 seconds (8257.12 seconds total)