Starting phenix.real_space_refine on Sun Sep 29 13:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2r_50981/09_2024/9g2r_50981.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2r_50981/09_2024/9g2r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2r_50981/09_2024/9g2r_50981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2r_50981/09_2024/9g2r_50981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2r_50981/09_2024/9g2r_50981.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g2r_50981/09_2024/9g2r_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 13.89, per 1000 atoms: 0.61 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: 5.86 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: 1.61 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: 7.30 Time building geometry restraints manager: 6.74 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: 0.00 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 49.680 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.870 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 14 poor density : 250 time to evaluate : 2.861 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: 0.3334 time to fit residues: 134.9250 Evaluate side-chains 106 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 2.686 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: 0.7603 (tmm) cc_final: 0.7207 (ttm) REVERT: C 179 LEU cc_start: 0.8690 (tp) cc_final: 0.8382 (pp) REVERT: C 229 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8515 (t0) REVERT: E 227 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8957 (pp) REVERT: F 60 MET cc_start: 0.9124 (ttm) cc_final: 0.8920 (ppp) REVERT: G 60 MET cc_start: 0.8665 (tpp) cc_final: 0.8395 (tpp) REVERT: H 237 TYR cc_start: 0.8195 (t80) cc_final: 0.7984 (t80) outliers start: 25 outliers final: 9 residues processed: 132 average time/residue: 0.2987 time to fit residues: 66.3564 Evaluate side-chains 98 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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 139 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 GLN F 116 ASN ** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN H 243 GLN I 222 HIS I 249 GLN J 116 ASN ** L 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22924 Z= 0.272 Angle : 0.610 12.092 30844 Z= 0.320 Chirality : 0.035 0.199 3488 Planarity : 0.004 0.047 4012 Dihedral : 3.213 18.297 3068 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.40 % Allowed : 8.31 % Favored : 90.29 % 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: 4.79 (0.14), residues: 2784 helix: 3.37 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.45 (0.38), residues: 212 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 0.028 0.002 TYR D 238 ARG 0.007 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 128 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 2.615 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 235 MET cc_start: 0.8594 (tmm) cc_final: 0.8208 (tmm) REVERT: C 60 MET cc_start: 0.7594 (tmm) cc_final: 0.7279 (ttm) REVERT: C 179 LEU cc_start: 0.8917 (tp) cc_final: 0.8558 (pp) REVERT: D 120 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8758 (mmtm) REVERT: G 60 MET cc_start: 0.8628 (tpp) cc_final: 0.8276 (tpp) REVERT: G 235 MET cc_start: 0.9030 (tmm) cc_final: 0.8444 (tmm) REVERT: H 237 TYR cc_start: 0.8297 (t80) cc_final: 0.8001 (t80) outliers start: 34 outliers final: 25 residues processed: 120 average time/residue: 0.3009 time to fit residues: 60.8054 Evaluate side-chains 106 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 2.749 ------------------------------------------------------------------------------- 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 125 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain 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 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 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 248 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 238 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 HIS ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 GLN K 228 ASN K 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4768 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= 0.232 Angle : 0.544 11.960 30844 Z= 0.286 Chirality : 0.033 0.143 3488 Planarity : 0.003 0.038 4012 Dihedral : 3.181 17.046 3068 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 1.45 % Allowed : 9.13 % Favored : 89.42 % 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: 3.60 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.41 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 55 HIS 0.006 0.001 HIS I 41 PHE 0.026 0.002 PHE I 230 TYR 0.030 0.002 TYR L 238 ARG 0.004 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 119 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 84 time to evaluate : 2.605 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: C 60 MET cc_start: 0.7615 (tmm) cc_final: 0.7270 (ttm) REVERT: C 179 LEU cc_start: 0.8916 (tp) cc_final: 0.8559 (pp) REVERT: D 120 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8735 (mmtm) REVERT: E 245 MET cc_start: 0.8732 (ttm) cc_final: 0.8288 (ttt) REVERT: F 235 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8146 (mmt) REVERT: G 60 MET cc_start: 0.8648 (tpp) cc_final: 0.8345 (tpp) REVERT: G 101 MET cc_start: 0.8436 (ptt) cc_final: 0.8221 (ptt) REVERT: G 245 MET cc_start: 0.9092 (ttm) cc_final: 0.8762 (ttm) REVERT: H 237 TYR cc_start: 0.8173 (t80) cc_final: 0.7816 (t80) REVERT: J 60 MET cc_start: 0.8423 (mmm) cc_final: 0.8173 (mmm) REVERT: J 245 MET cc_start: 0.7820 (tpp) cc_final: 0.6175 (tpp) outliers start: 35 outliers final: 28 residues processed: 113 average time/residue: 0.2918 time to fit residues: 55.8097 Evaluate side-chains 108 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 252 LEU 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 120 LYS Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain J residue 19 LEU 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 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 222 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 110 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN G 222 HIS ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 243 GLN ** K 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5315 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= 0.240 Angle : 0.556 9.692 30844 Z= 0.291 Chirality : 0.033 0.262 3488 Planarity : 0.003 0.039 4012 Dihedral : 3.216 19.694 3068 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.98 % Allowed : 9.75 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.02 (0.14), residues: 2784 helix: 3.55 (0.09), residues: 2568 sheet: None (None), residues: 0 loop : -0.59 (0.38), residues: 216 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 0.024 0.002 PHE I 230 TYR 0.034 0.002 TYR G 155 ARG 0.005 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 130 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 82 time to evaluate : 3.223 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 235 MET cc_start: 0.8409 (tmm) cc_final: 0.8057 (tmm) REVERT: C 60 MET cc_start: 0.7656 (tmm) cc_final: 0.7323 (ttm) REVERT: C 179 LEU cc_start: 0.8961 (tp) cc_final: 0.8596 (pp) REVERT: D 60 MET cc_start: 0.8135 (ttt) cc_final: 0.7612 (tmm) REVERT: E 60 MET cc_start: 0.9166 (ppp) cc_final: 0.8965 (ppp) REVERT: E 245 MET cc_start: 0.8687 (ttm) cc_final: 0.8370 (ttt) REVERT: F 235 MET cc_start: 0.8553 (mmm) cc_final: 0.8259 (mmt) REVERT: G 60 MET cc_start: 0.8677 (tpp) cc_final: 0.8385 (tpp) REVERT: H 237 TYR cc_start: 0.8165 (t80) cc_final: 0.7793 (t80) REVERT: I 65 VAL cc_start: 0.9340 (t) cc_final: 0.9135 (p) REVERT: L 245 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5199 (ppp) outliers start: 48 outliers final: 30 residues processed: 120 average time/residue: 0.3217 time to fit residues: 64.4651 Evaluate side-chains 107 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 76 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 125 GLN 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 I residue 147 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 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 89 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 267 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 GLN H 222 HIS I 243 GLN ** K 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22924 Z= 0.268 Angle : 0.587 10.014 30844 Z= 0.309 Chirality : 0.035 0.210 3488 Planarity : 0.004 0.041 4012 Dihedral : 3.314 18.973 3068 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.98 % Allowed : 10.66 % Favored : 87.36 % 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: 4.79 (0.14), residues: 2784 helix: 3.38 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.43 (0.40), residues: 212 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 0.018 0.002 PHE J 143 TYR 0.036 0.002 TYR I 237 ARG 0.006 0.001 ARG E 225 *********************** 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 127 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 79 time to evaluate : 2.614 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: B 235 MET cc_start: 0.8444 (tmm) cc_final: 0.7995 (tmm) REVERT: C 60 MET cc_start: 0.7664 (tmm) cc_final: 0.7343 (ttm) REVERT: C 179 LEU cc_start: 0.8926 (tp) cc_final: 0.8579 (pp) REVERT: D 60 MET cc_start: 0.8183 (ttt) cc_final: 0.7709 (tmm) REVERT: E 245 MET cc_start: 0.8689 (ttm) cc_final: 0.8364 (ttt) REVERT: F 235 MET cc_start: 0.8584 (mmm) cc_final: 0.8252 (mmt) REVERT: G 60 MET cc_start: 0.8681 (tpp) cc_final: 0.8417 (tpp) REVERT: G 101 MET cc_start: 0.8329 (ptt) cc_final: 0.7980 (ptt) REVERT: G 245 MET cc_start: 0.9153 (ttm) cc_final: 0.8797 (ttm) REVERT: H 237 TYR cc_start: 0.8167 (t80) cc_final: 0.7803 (t80) REVERT: I 230 PHE cc_start: 0.8034 (t80) cc_final: 0.7830 (t80) REVERT: L 245 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5982 (ppp) outliers start: 48 outliers final: 34 residues processed: 120 average time/residue: 0.3145 time to fit residues: 63.3248 Evaluate side-chains 107 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 72 time to evaluate : 2.650 ------------------------------------------------------------------------------- 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 231 VAL 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 B residue 231 VAL Chi-restraints excluded: chain B residue 252 LEU 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 D residue 231 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 230 PHE Chi-restraints excluded: chain K residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 ASN K 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5984 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= 0.166 Angle : 0.523 11.467 30844 Z= 0.271 Chirality : 0.033 0.221 3488 Planarity : 0.003 0.041 4012 Dihedral : 3.172 21.444 3068 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 1.40 % Allowed : 11.53 % Favored : 87.07 % 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 (0.15), residues: 2784 helix: 3.78 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.39 (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 0.035 0.001 PHE I 143 TYR 0.025 0.001 TYR K 100 ARG 0.004 0.000 ARG L 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 116 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 82 time to evaluate : 2.563 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: B 235 MET cc_start: 0.8443 (tmm) cc_final: 0.8101 (tmm) REVERT: C 60 MET cc_start: 0.7667 (tmm) cc_final: 0.7358 (ttp) REVERT: D 60 MET cc_start: 0.8076 (ttt) cc_final: 0.7812 (ttt) REVERT: G 60 MET cc_start: 0.8688 (tpp) cc_final: 0.8412 (tpp) REVERT: G 101 MET cc_start: 0.8340 (ptt) cc_final: 0.8063 (ptt) REVERT: G 245 MET cc_start: 0.9046 (ttm) cc_final: 0.8789 (ttm) REVERT: I 101 MET cc_start: 0.8733 (pmm) cc_final: 0.8460 (pmm) REVERT: J 60 MET cc_start: 0.8453 (mmm) cc_final: 0.8166 (mmm) REVERT: J 114 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: L 245 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5964 (ptm) outliers start: 34 outliers final: 22 residues processed: 109 average time/residue: 0.3077 time to fit residues: 56.5509 Evaluate side-chains 96 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 2.689 ------------------------------------------------------------------------------- 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 125 GLN Chi-restraints excluded: chain C residue 128 ILE 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 67 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 H residue 67 LEU Chi-restraints excluded: chain J residue 114 TYR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 242 TYR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 245 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 158 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN K 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22924 Z= 0.163 Angle : 0.536 12.176 30844 Z= 0.274 Chirality : 0.032 0.191 3488 Planarity : 0.003 0.041 4012 Dihedral : 3.175 22.793 3068 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.24 % Allowed : 12.02 % Favored : 86.74 % 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: 5.53 (0.15), residues: 2784 helix: 3.87 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 55 HIS 0.005 0.001 HIS I 41 PHE 0.032 0.001 PHE I 230 TYR 0.035 0.002 TYR J 100 ARG 0.003 0.000 ARG L 178 *********************** 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 110 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8574 (tmm) cc_final: 0.8029 (tmm) REVERT: B 235 MET cc_start: 0.8426 (tmm) cc_final: 0.8084 (tmm) REVERT: C 60 MET cc_start: 0.7706 (tmm) cc_final: 0.7397 (ttp) REVERT: E 245 MET cc_start: 0.8112 (ttt) cc_final: 0.7716 (ttt) REVERT: F 235 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7605 (mmt) REVERT: G 60 MET cc_start: 0.8638 (tpp) cc_final: 0.8347 (tpp) REVERT: G 101 MET cc_start: 0.8283 (ptt) cc_final: 0.7892 (ptt) REVERT: G 245 MET cc_start: 0.8956 (ttm) cc_final: 0.8683 (ttm) REVERT: H 237 TYR cc_start: 0.7886 (t80) cc_final: 0.7622 (t80) REVERT: J 60 MET cc_start: 0.8491 (mmm) cc_final: 0.8179 (mmm) REVERT: J 114 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: L 245 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6222 (ptm) outliers start: 30 outliers final: 23 residues processed: 104 average time/residue: 0.3052 time to fit residues: 54.1599 Evaluate side-chains 101 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 2.852 ------------------------------------------------------------------------------- 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 125 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 121 CYS Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain J residue 114 TYR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 41 HIS Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22924 Z= 0.287 Angle : 0.631 10.895 30844 Z= 0.331 Chirality : 0.035 0.201 3488 Planarity : 0.004 0.040 4012 Dihedral : 3.383 21.584 3068 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.49 % Allowed : 12.15 % Favored : 86.36 % 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: 4.80 (0.15), residues: 2784 helix: 3.38 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.40 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 55 HIS 0.010 0.001 HIS K 41 PHE 0.038 0.002 PHE I 230 TYR 0.046 0.002 TYR J 100 ARG 0.005 0.001 ARG E 225 *********************** 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 108 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 72 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.8487 (tmm) cc_final: 0.7931 (tmm) REVERT: C 60 MET cc_start: 0.7835 (tmm) cc_final: 0.7551 (ttp) REVERT: D 60 MET cc_start: 0.7862 (ttt) cc_final: 0.7623 (ttt) REVERT: E 245 MET cc_start: 0.8346 (ttt) cc_final: 0.6906 (ttt) REVERT: F 235 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7218 (tpt) REVERT: G 60 MET cc_start: 0.8679 (tpp) cc_final: 0.8255 (tpp) REVERT: G 101 MET cc_start: 0.8546 (ptt) cc_final: 0.8146 (ptt) REVERT: H 235 MET cc_start: 0.8694 (tmm) cc_final: 0.8409 (tmm) REVERT: J 60 MET cc_start: 0.8515 (mmm) cc_final: 0.8105 (mmm) REVERT: J 114 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: L 245 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6019 (ptm) outliers start: 36 outliers final: 27 residues processed: 104 average time/residue: 0.2935 time to fit residues: 52.1295 Evaluate side-chains 96 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 66 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 128 ILE 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 D residue 231 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain J residue 114 TYR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 67 LEU 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 143 PHE Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 245 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 182 optimal weight: 50.0000 chunk 274 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 173 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22924 Z= 0.241 Angle : 0.605 13.922 30844 Z= 0.317 Chirality : 0.035 0.243 3488 Planarity : 0.003 0.039 4012 Dihedral : 3.390 22.122 3068 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.20 % Allowed : 12.48 % Favored : 86.32 % 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: 4.87 (0.15), residues: 2784 helix: 3.43 (0.09), residues: 2576 sheet: None (None), residues: 0 loop : -0.46 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 55 HIS 0.005 0.001 HIS K 223 PHE 0.044 0.002 PHE J 143 TYR 0.050 0.002 TYR K 100 ARG 0.004 0.001 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 fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 MET cc_start: 0.8457 (tmm) cc_final: 0.7981 (tmm) REVERT: C 60 MET cc_start: 0.7865 (tmm) cc_final: 0.7552 (ttp) REVERT: E 235 MET cc_start: 0.7977 (tpp) cc_final: 0.7318 (mmm) REVERT: E 245 MET cc_start: 0.8342 (ttt) cc_final: 0.7603 (ttt) REVERT: F 235 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7579 (mmt) REVERT: G 60 MET cc_start: 0.8662 (tpp) cc_final: 0.8352 (tpp) REVERT: G 101 MET cc_start: 0.8536 (ptt) cc_final: 0.8118 (ptt) REVERT: G 245 MET cc_start: 0.9158 (ttm) cc_final: 0.8900 (ttm) REVERT: J 60 MET cc_start: 0.8346 (mmm) cc_final: 0.7931 (mmm) REVERT: J 101 MET cc_start: 0.7953 (ppp) cc_final: 0.7716 (ppp) REVERT: J 114 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.7054 (m-80) REVERT: L 245 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6185 (ptm) outliers start: 29 outliers final: 25 residues processed: 93 average time/residue: 0.3274 time to fit residues: 52.2005 Evaluate side-chains 96 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 68 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain C residue 121 CYS Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 230 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 114 TYR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain K residue 67 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 222 HIS E 234 GLN K 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.057064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.044049 restraints weight = 204259.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.042813 restraints weight = 110897.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.043117 restraints weight = 89925.872| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22924 Z= 0.172 Angle : 0.581 16.481 30844 Z= 0.298 Chirality : 0.034 0.318 3488 Planarity : 0.003 0.040 4012 Dihedral : 3.300 22.160 3068 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.16 % Allowed : 12.52 % Favored : 86.32 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.33 (0.15), residues: 2784 helix: 3.74 (0.09), residues: 2572 sheet: None (None), residues: 0 loop : -0.42 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 55 HIS 0.005 0.001 HIS K 223 PHE 0.041 0.001 PHE I 230 TYR 0.038 0.002 TYR J 100 ARG 0.004 0.000 ARG H 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2972.56 seconds wall clock time: 55 minutes 42.67 seconds (3342.67 seconds total)