Starting phenix.real_space_refine on Fri Jan 24 23:59:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g2r_50981/01_2025/9g2r_50981.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g2r_50981/01_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_50981/01_2025/9g2r_50981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g2r_50981/01_2025/9g2r_50981.map" model { file = "/net/cci-nas-00/data/ceres_data/9g2r_50981/01_2025/9g2r_50981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g2r_50981/01_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-5571/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: 12.45, per 1000 atoms: 0.55 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: 5.36 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: 1.55 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: 7.07 Time building geometry restraints manager: 6.15 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: 0.04 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 45.400 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.650 ------------------------------------------------------------------------------- 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= 0.630 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 *********************** 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 : 2.690 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: 0.3500 time to fit residues: 141.8679 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 : 2.841 ------------------------------------------------------------------------------- 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 = 197687.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.046714 restraints weight = 95277.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.046859 restraints weight = 75422.918| |-----------------------------------------------------------------------------| 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= 0.212 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 *********************** 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 : 2.716 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: 0.7486 (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: 0.8269 (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: 0.3181 time to fit residues: 70.1370 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 : 2.606 ------------------------------------------------------------------------------- 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: 7.9990 chunk 27 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 GLN F 116 ASN H 116 ASN H 243 GLN I 249 GLN J 116 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.059002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.042627 restraints weight = 200321.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.043377 restraints weight = 91779.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.043871 restraints weight = 49961.503| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22924 Z= 0.231 Angle : 0.566 11.860 30844 Z= 0.296 Chirality : 0.034 0.202 3488 Planarity : 0.004 0.040 4012 Dihedral : 3.093 17.623 3068 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 5.13 (0.14), residues: 2784 helix: 3.61 (0.09), residues: 2576 sheet: None (None), residues: 0 loop : -0.61 (0.38), 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 0.020 0.002 PHE J 230 TYR 0.025 0.002 TYR L 238 ARG 0.005 0.001 ARG E 225 *********************** 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 126 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 2.779 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: B 60 MET cc_start: 0.8407 (ttp) cc_final: 0.8108 (ttt) REVERT: B 235 MET cc_start: 0.8442 (tmm) cc_final: 0.8103 (tmm) REVERT: C 60 MET cc_start: 0.7745 (tmm) cc_final: 0.7476 (ttm) REVERT: C 179 LEU cc_start: 0.9392 (tp) cc_final: 0.8978 (pp) REVERT: D 19 LEU cc_start: 0.9683 (mt) cc_final: 0.9470 (pp) REVERT: E 101 MET cc_start: 0.8805 (ptp) cc_final: 0.8568 (ptp) REVERT: F 235 MET cc_start: 0.8575 (tpp) cc_final: 0.8347 (mmm) REVERT: G 60 MET cc_start: 0.9041 (tpp) cc_final: 0.8690 (tpp) REVERT: G 245 MET cc_start: 0.9074 (tpp) cc_final: 0.8648 (ttm) REVERT: H 237 TYR cc_start: 0.8505 (t80) cc_final: 0.8064 (t80) REVERT: I 235 MET cc_start: 0.9308 (tpp) cc_final: 0.8417 (tpp) REVERT: J 238 TYR cc_start: 0.9340 (OUTLIER) cc_final: 0.8993 (m-10) REVERT: J 245 MET cc_start: 0.8946 (tpt) cc_final: 0.7819 (tpt) REVERT: K 237 TYR cc_start: 0.9153 (OUTLIER) cc_final: 0.8708 (t80) REVERT: L 60 MET cc_start: 0.9471 (ptt) cc_final: 0.9197 (ptt) outliers start: 31 outliers final: 23 residues processed: 118 average time/residue: 0.3075 time to fit residues: 61.6211 Evaluate side-chains 110 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 I residue 147 LEU 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: 0.9980 chunk 201 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 HIS K 228 ASN ** K 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.057652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.041089 restraints weight = 205357.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.042053 restraints weight = 106639.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.042055 restraints weight = 58232.718| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4990 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= 0.245 Angle : 0.554 9.491 30844 Z= 0.293 Chirality : 0.034 0.151 3488 Planarity : 0.004 0.038 4012 Dihedral : 3.219 17.364 3068 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.53 % Allowed : 8.76 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.09 (0.14), residues: 2784 helix: 3.57 (0.09), residues: 2576 sheet: None (None), residues: 0 loop : -0.50 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 55 HIS 0.006 0.001 HIS I 41 PHE 0.029 0.002 PHE I 230 TYR 0.030 0.002 TYR G 155 ARG 0.005 0.001 ARG K 225 *********************** 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 127 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 90 time to evaluate : 2.855 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: A 235 MET cc_start: 0.8572 (tmm) cc_final: 0.8150 (tmm) REVERT: C 179 LEU cc_start: 0.9399 (tp) cc_final: 0.8975 (pp) REVERT: E 245 MET cc_start: 0.9047 (ttm) cc_final: 0.8328 (ttt) REVERT: F 235 MET cc_start: 0.8644 (tpp) cc_final: 0.8230 (tpt) REVERT: G 60 MET cc_start: 0.9013 (tpp) cc_final: 0.8701 (tpp) REVERT: G 101 MET cc_start: 0.8653 (ptt) cc_final: 0.8343 (ptt) REVERT: G 245 MET cc_start: 0.9020 (tpp) cc_final: 0.8571 (ttm) REVERT: H 237 TYR cc_start: 0.8418 (t80) cc_final: 0.7994 (t80) REVERT: J 60 MET cc_start: 0.9569 (mmm) cc_final: 0.9118 (mmm) REVERT: J 245 MET cc_start: 0.8932 (tpt) cc_final: 0.8571 (tpp) REVERT: K 97 LEU cc_start: 0.9689 (tp) cc_final: 0.9215 (mt) REVERT: K 143 PHE cc_start: 0.9566 (t80) cc_final: 0.9273 (m-80) REVERT: K 237 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8747 (t80) REVERT: L 60 MET cc_start: 0.9458 (ptt) cc_final: 0.9197 (ptt) outliers start: 37 outliers final: 27 residues processed: 118 average time/residue: 0.3184 time to fit residues: 62.6802 Evaluate side-chains 108 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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 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 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 79 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 I residue 84 ASP 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: 1.9990 chunk 140 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 223 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN K 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.057660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.041708 restraints weight = 203612.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.041872 restraints weight = 116090.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.042142 restraints weight = 66272.966| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22924 Z= 0.199 Angle : 0.512 12.378 30844 Z= 0.266 Chirality : 0.032 0.149 3488 Planarity : 0.003 0.045 4012 Dihedral : 3.125 16.906 3068 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.74 % Allowed : 9.59 % Favored : 88.68 % 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: 5.40 (0.14), residues: 2784 helix: 3.78 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.36 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 55 HIS 0.006 0.001 HIS I 41 PHE 0.021 0.001 PHE J 230 TYR 0.028 0.002 TYR G 155 ARG 0.003 0.001 ARG E 225 *********************** 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 126 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 2.730 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: A 235 MET cc_start: 0.8432 (tmm) cc_final: 0.8012 (tmm) REVERT: B 235 MET cc_start: 0.8250 (tmm) cc_final: 0.7960 (tmm) REVERT: C 60 MET cc_start: 0.8096 (ttp) cc_final: 0.7106 (tmm) REVERT: C 179 LEU cc_start: 0.9333 (tp) cc_final: 0.8904 (pp) REVERT: D 60 MET cc_start: 0.8220 (ttt) cc_final: 0.7436 (tmm) REVERT: G 60 MET cc_start: 0.9018 (tpp) cc_final: 0.8715 (tpp) REVERT: G 101 MET cc_start: 0.8604 (ptt) cc_final: 0.8278 (ptt) REVERT: G 245 MET cc_start: 0.9140 (tpp) cc_final: 0.8562 (ttm) REVERT: H 237 TYR cc_start: 0.8388 (t80) cc_final: 0.7894 (t80) REVERT: H 245 MET cc_start: 0.9364 (tpp) cc_final: 0.8997 (ttm) REVERT: J 60 MET cc_start: 0.9590 (mmm) cc_final: 0.9105 (mmm) REVERT: J 245 MET cc_start: 0.8890 (tpt) cc_final: 0.8540 (tpp) REVERT: K 143 PHE cc_start: 0.9528 (t80) cc_final: 0.9253 (m-80) REVERT: K 237 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8567 (t80) REVERT: L 60 MET cc_start: 0.9446 (ptt) cc_final: 0.9129 (ptm) REVERT: L 245 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6004 (ppp) outliers start: 42 outliers final: 28 residues processed: 116 average time/residue: 0.3224 time to fit residues: 62.6114 Evaluate side-chains 107 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 MET 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 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 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 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 84 ASP 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 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 Chi-restraints excluded: chain L residue 245 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 96 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 182 optimal weight: 50.0000 chunk 159 optimal weight: 0.0370 chunk 98 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 222 HIS H 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.058135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.043449 restraints weight = 201303.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.043280 restraints weight = 113134.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.043255 restraints weight = 77340.316| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22924 Z= 0.146 Angle : 0.489 11.599 30844 Z= 0.249 Chirality : 0.031 0.275 3488 Planarity : 0.003 0.042 4012 Dihedral : 3.062 17.877 3068 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.53 % Allowed : 10.08 % Favored : 88.39 % 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: 5.82 (0.14), residues: 2784 helix: 4.06 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.33 (0.39), 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 0.021 0.001 PHE J 230 TYR 0.031 0.001 TYR G 155 ARG 0.007 0.000 ARG H 178 *********************** 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 119 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 2.735 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: 0.8521 (tmm) cc_final: 0.7994 (tmm) REVERT: A 247 ASP cc_start: 0.8985 (m-30) cc_final: 0.8656 (t70) REVERT: B 235 MET cc_start: 0.8189 (tmm) cc_final: 0.7942 (tmm) REVERT: C 60 MET cc_start: 0.8020 (ttp) cc_final: 0.7043 (tmm) REVERT: C 179 LEU cc_start: 0.9293 (tp) cc_final: 0.8871 (pp) REVERT: D 60 MET cc_start: 0.8049 (ttt) cc_final: 0.7552 (tmm) REVERT: E 245 MET cc_start: 0.8937 (ttm) cc_final: 0.8565 (ttt) REVERT: G 60 MET cc_start: 0.9047 (tpp) cc_final: 0.8787 (tpp) REVERT: H 237 TYR cc_start: 0.8206 (t80) cc_final: 0.7932 (t80) REVERT: H 245 MET cc_start: 0.9307 (tpp) cc_final: 0.9088 (ttm) REVERT: I 238 TYR cc_start: 0.9381 (OUTLIER) cc_final: 0.9000 (t80) REVERT: J 60 MET cc_start: 0.9586 (mmm) cc_final: 0.9095 (mmm) REVERT: J 114 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: J 235 MET cc_start: 0.9308 (ppp) cc_final: 0.9105 (ppp) REVERT: J 245 MET cc_start: 0.8995 (tpt) cc_final: 0.8684 (tpp) REVERT: K 143 PHE cc_start: 0.9548 (t80) cc_final: 0.9246 (m-80) REVERT: K 237 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8664 (t80) REVERT: L 60 MET cc_start: 0.9451 (ptt) cc_final: 0.9135 (ptm) outliers start: 37 outliers final: 23 residues processed: 113 average time/residue: 0.3182 time to fit residues: 60.4271 Evaluate side-chains 101 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 2.721 ------------------------------------------------------------------------------- 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 231 VAL 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 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 227 LEU Chi-restraints excluded: chain E residue 230 PHE 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 67 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 238 TYR 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 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 188 ARG 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: 7.9990 chunk 5 optimal weight: 6.9990 chunk 184 optimal weight: 0.0670 chunk 54 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 overall best weight: 0.9924 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.058635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.042732 restraints weight = 203129.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.042950 restraints weight = 105296.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.043516 restraints weight = 67438.408| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22924 Z= 0.133 Angle : 0.485 10.152 30844 Z= 0.244 Chirality : 0.032 0.294 3488 Planarity : 0.003 0.041 4012 Dihedral : 3.004 19.574 3068 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.28 % Allowed : 10.37 % Favored : 88.35 % 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: 6.05 (0.14), residues: 2784 helix: 4.21 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.34 (0.39), 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 0.022 0.001 PHE J 230 TYR 0.035 0.001 TYR G 155 ARG 0.003 0.000 ARG J 178 *********************** 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 121 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 2.726 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: 0.8522 (tmm) cc_final: 0.8056 (tmm) REVERT: A 247 ASP cc_start: 0.8939 (m-30) cc_final: 0.8644 (t70) REVERT: C 60 MET cc_start: 0.8101 (ttp) cc_final: 0.7088 (tmm) REVERT: C 179 LEU cc_start: 0.9279 (tp) cc_final: 0.8861 (pp) REVERT: D 125 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8357 (tp40) REVERT: E 245 MET cc_start: 0.8896 (ttm) cc_final: 0.8644 (ttt) REVERT: G 60 MET cc_start: 0.9073 (tpp) cc_final: 0.8830 (tpp) REVERT: H 237 TYR cc_start: 0.8289 (t80) cc_final: 0.8046 (t80) REVERT: H 245 MET cc_start: 0.9279 (tpp) cc_final: 0.8944 (ttm) REVERT: I 245 MET cc_start: 0.9468 (ttt) cc_final: 0.9137 (ptm) REVERT: J 60 MET cc_start: 0.9617 (mmm) cc_final: 0.9148 (mmm) REVERT: J 114 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8324 (m-80) REVERT: J 245 MET cc_start: 0.8900 (tpt) cc_final: 0.8536 (tpt) REVERT: K 143 PHE cc_start: 0.9579 (t80) cc_final: 0.9280 (m-80) REVERT: L 60 MET cc_start: 0.9428 (ptt) cc_final: 0.9159 (ptm) outliers start: 31 outliers final: 19 residues processed: 115 average time/residue: 0.3062 time to fit residues: 59.0512 Evaluate side-chains 96 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 2.560 ------------------------------------------------------------------------------- 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 C residue 121 CYS 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 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain L residue 188 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 59 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 212 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 GLN G 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.057164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.041761 restraints weight = 203361.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.041860 restraints weight = 101817.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.041923 restraints weight = 69551.308| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22924 Z= 0.229 Angle : 0.569 13.529 30844 Z= 0.293 Chirality : 0.033 0.232 3488 Planarity : 0.003 0.038 4012 Dihedral : 3.123 16.965 3068 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.12 % Allowed : 10.99 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.52 (0.14), residues: 2784 helix: 3.86 (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 0.007 0.001 TRP C 55 HIS 0.010 0.001 HIS K 41 PHE 0.020 0.002 PHE J 230 TYR 0.021 0.002 TYR J 100 ARG 0.005 0.001 ARG E 225 *********************** 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 98 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 2.876 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 245 MET cc_start: 0.8428 (ttm) cc_final: 0.8013 (ttm) REVERT: C 179 LEU cc_start: 0.9288 (tp) cc_final: 0.8851 (pp) REVERT: D 60 MET cc_start: 0.8026 (ttt) cc_final: 0.7763 (ttt) REVERT: E 235 MET cc_start: 0.8764 (tpp) cc_final: 0.7980 (mmm) REVERT: E 245 MET cc_start: 0.9027 (ttm) cc_final: 0.8738 (ttt) REVERT: G 60 MET cc_start: 0.8945 (tpp) cc_final: 0.8578 (tpp) REVERT: H 235 MET cc_start: 0.8867 (tmm) cc_final: 0.8631 (tmm) REVERT: J 60 MET cc_start: 0.9589 (mmm) cc_final: 0.9103 (mmm) REVERT: J 114 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: J 245 MET cc_start: 0.8957 (tpt) cc_final: 0.8619 (tpt) REVERT: K 97 LEU cc_start: 0.9618 (tp) cc_final: 0.9114 (mt) REVERT: K 143 PHE cc_start: 0.9523 (t80) cc_final: 0.9259 (m-80) REVERT: L 60 MET cc_start: 0.9441 (ptt) cc_final: 0.9189 (ptm) outliers start: 27 outliers final: 20 residues processed: 94 average time/residue: 0.3248 time to fit residues: 51.3855 Evaluate side-chains 91 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 2.585 ------------------------------------------------------------------------------- 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 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 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 L residue 83 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: 5.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 229 optimal weight: 40.0000 chunk 185 optimal weight: 7.9990 chunk 142 optimal weight: 0.0370 chunk 249 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 GLN K 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.057849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.044502 restraints weight = 201987.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.043393 restraints weight = 107767.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.043626 restraints weight = 88294.652| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22924 Z= 0.147 Angle : 0.523 12.816 30844 Z= 0.263 Chirality : 0.032 0.219 3488 Planarity : 0.003 0.037 4012 Dihedral : 3.059 16.545 3068 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.03 % Allowed : 10.95 % Favored : 88.02 % 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: 5.86 (0.15), residues: 2784 helix: 4.09 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.34 (0.40), 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 0.021 0.001 PHE J 230 TYR 0.018 0.001 TYR J 100 ARG 0.003 0.000 ARG L 178 *********************** 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 104 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 2.676 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 247 ASP cc_start: 0.8949 (m-30) cc_final: 0.8525 (t70) REVERT: A 252 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7563 (mm) REVERT: C 179 LEU cc_start: 0.9259 (tp) cc_final: 0.8837 (pp) REVERT: D 60 MET cc_start: 0.7975 (ttt) cc_final: 0.7699 (ttt) REVERT: E 235 MET cc_start: 0.8742 (tpp) cc_final: 0.8107 (mmm) REVERT: E 245 MET cc_start: 0.8944 (ttm) cc_final: 0.8676 (ttt) REVERT: I 245 MET cc_start: 0.9455 (ttt) cc_final: 0.9118 (ptm) REVERT: J 60 MET cc_start: 0.9601 (mmm) cc_final: 0.9096 (mmm) REVERT: J 114 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: J 245 MET cc_start: 0.8964 (tpt) cc_final: 0.8621 (tpt) REVERT: K 97 LEU cc_start: 0.9598 (tp) cc_final: 0.9098 (mt) REVERT: K 143 PHE cc_start: 0.9537 (t80) cc_final: 0.9254 (m-80) REVERT: L 60 MET cc_start: 0.9440 (ptt) cc_final: 0.9186 (ptm) outliers start: 25 outliers final: 20 residues processed: 100 average time/residue: 0.3100 time to fit residues: 52.5278 Evaluate side-chains 95 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 2.735 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain B residue 231 VAL 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 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 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 237 TYR 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: 3.9990 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 182 optimal weight: 50.0000 chunk 272 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.057018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.040854 restraints weight = 203817.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.041138 restraints weight = 114166.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.041734 restraints weight = 67033.417| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.6455 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= 0.201 Angle : 0.558 12.131 30844 Z= 0.287 Chirality : 0.033 0.202 3488 Planarity : 0.003 0.035 4012 Dihedral : 3.134 16.344 3068 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.12 % Allowed : 10.99 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.54 (0.15), residues: 2784 helix: 3.87 (0.09), residues: 2576 sheet: None (None), residues: 0 loop : -0.37 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 55 HIS 0.009 0.001 HIS K 41 PHE 0.023 0.001 PHE J 230 TYR 0.038 0.002 TYR L 100 ARG 0.004 0.000 ARG E 225 ********************** 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: 27 poor density : 72 time to evaluate : 2.659 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: C 179 LEU cc_start: 0.9288 (tp) cc_final: 0.8891 (pp) REVERT: D 60 MET cc_start: 0.7970 (ttt) cc_final: 0.7704 (ttt) REVERT: E 235 MET cc_start: 0.8923 (tpp) cc_final: 0.8243 (mmm) REVERT: E 245 MET cc_start: 0.9024 (ttm) cc_final: 0.7625 (ttt) REVERT: F 235 MET cc_start: 0.8742 (tpp) cc_final: 0.7917 (tpp) REVERT: H 101 MET cc_start: 0.8879 (ttp) cc_final: 0.8498 (tmm) REVERT: H 235 MET cc_start: 0.8906 (tmm) cc_final: 0.8558 (tmm) REVERT: I 245 MET cc_start: 0.9548 (ttt) cc_final: 0.9145 (ptm) REVERT: J 60 MET cc_start: 0.9626 (mmm) cc_final: 0.9088 (mmm) REVERT: J 114 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8412 (m-80) REVERT: J 245 MET cc_start: 0.8975 (tpt) cc_final: 0.8621 (tpt) REVERT: K 97 LEU cc_start: 0.9606 (tp) cc_final: 0.9081 (mt) REVERT: K 100 TYR cc_start: 0.9301 (m-10) cc_final: 0.9096 (m-10) REVERT: K 143 PHE cc_start: 0.9628 (t80) cc_final: 0.9370 (m-80) REVERT: L 60 MET cc_start: 0.9434 (ptt) cc_final: 0.9198 (ptm) outliers start: 27 outliers final: 21 residues processed: 97 average time/residue: 0.3097 time to fit residues: 51.6573 Evaluate side-chains 93 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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 125 GLN 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 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 121 CYS 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 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 237 TYR Chi-restraints excluded: chain L residue 83 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: 8.9990 chunk 253 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 229 optimal weight: 50.0000 chunk 185 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 246 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 182 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN D 41 HIS D 228 ASN G 251 GLN H 222 HIS J 243 GLN K 41 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.055901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.040583 restraints weight = 204149.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.039859 restraints weight = 120620.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.040549 restraints weight = 73585.922| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22924 Z= 0.321 Angle : 0.664 11.691 30844 Z= 0.348 Chirality : 0.037 0.238 3488 Planarity : 0.004 0.036 4012 Dihedral : 3.469 19.474 3068 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.95 % Allowed : 11.28 % Favored : 87.77 % 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: 4.60 (0.15), residues: 2784 helix: 3.23 (0.09), residues: 2584 sheet: None (None), residues: 0 loop : -0.41 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 55 HIS 0.006 0.001 HIS G 223 PHE 0.023 0.002 PHE J 230 TYR 0.032 0.002 TYR L 100 ARG 0.006 0.001 ARG E 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6457.92 seconds wall clock time: 117 minutes 52.79 seconds (7072.79 seconds total)