Starting phenix.real_space_refine on Sun Apr 7 02:05:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/04_2024/7vuh_32128_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/04_2024/7vuh_32128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/04_2024/7vuh_32128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/04_2024/7vuh_32128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/04_2024/7vuh_32128_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/04_2024/7vuh_32128_updated.pdb" } resolution = 3.22 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 1 4.86 5 C 5292 2.51 5 N 1436 2.21 5 O 1523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8302 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1970 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2335 Unusual residues: {'7ZQ': 1} Classifications: {'peptide': 282, 'undetermined': 1} Link IDs: {'PTRANS': 12, 'TRANS': 269, None: 1} Not linked: pdbres="PHE R 304 " pdbres="7ZQ R 401 " Time building chain proxies: 4.72, per 1000 atoms: 0.57 Number of scatterers: 8302 At special positions: 0 Unit cell: (76.96, 99.84, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 50 16.00 O 1523 8.00 N 1436 7.00 C 5292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.14 Conformation dependent library (CDL) restraints added in 1.6 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 11 sheets defined 35.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 10 through 37 removed outlier: 3.734A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.649A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 24 through 53 Proline residue: R 29 - end of helix Proline residue: R 42 - end of helix removed outlier: 3.843A pdb=" N GLN R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 58 removed outlier: 3.614A pdb=" N ARG R 58 " --> pdb=" O VAL R 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 55 through 58' Processing helix chain 'R' and resid 61 through 82 removed outlier: 3.844A pdb=" N VAL R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 90 No H-bonds generated for 'chain 'R' and resid 87 through 90' Processing helix chain 'R' and resid 102 through 131 removed outlier: 3.594A pdb=" N LEU R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 144 through 159 removed outlier: 3.645A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR R 153 " --> pdb=" O ILE R 149 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE R 154 " --> pdb=" O VAL R 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 191 Processing helix chain 'R' and resid 193 through 211 removed outlier: 4.003A pdb=" N LEU R 202 " --> pdb=" O ILE R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 253 removed outlier: 4.214A pdb=" N THR R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 243 - end of helix removed outlier: 3.955A pdb=" N LEU R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 261 No H-bonds generated for 'chain 'R' and resid 259 through 261' Processing helix chain 'R' and resid 263 through 283 removed outlier: 3.686A pdb=" N THR R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 299 Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 6.895A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.064A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.478A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.629A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 191 removed outlier: 3.554A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.612A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.655A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.570A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 18 through 20 removed outlier: 3.719A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 95 through 98 removed outlier: 3.677A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1334 1.31 - 1.44: 2377 1.44 - 1.56: 4700 1.56 - 1.69: 0 1.69 - 1.82: 71 Bond restraints: 8482 Sorted by residual: bond pdb=" C9 7ZQ R 401 " pdb=" N2 7ZQ R 401 " ideal model delta sigma weight residual 1.341 1.447 -0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C7 7ZQ R 401 " pdb=" N1 7ZQ R 401 " ideal model delta sigma weight residual 1.344 1.448 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3 7ZQ R 401 " pdb="CL1 7ZQ R 401 " ideal model delta sigma weight residual 1.732 1.784 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C7 7ZQ R 401 " pdb=" O1 7ZQ R 401 " ideal model delta sigma weight residual 1.222 1.182 0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C9 7ZQ R 401 " pdb=" O2 7ZQ R 401 " ideal model delta sigma weight residual 1.219 1.180 0.039 2.00e-02 2.50e+03 3.77e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.78: 137 105.78 - 112.84: 4503 112.84 - 119.89: 2865 119.89 - 126.95: 3896 126.95 - 134.00: 101 Bond angle restraints: 11502 Sorted by residual: angle pdb=" N ILE R 118 " pdb=" CA ILE R 118 " pdb=" C ILE R 118 " ideal model delta sigma weight residual 111.81 107.53 4.28 8.60e-01 1.35e+00 2.47e+01 angle pdb=" C SER R 160 " pdb=" N ILE R 161 " pdb=" CA ILE R 161 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.79e+01 angle pdb=" C VAL R 191 " pdb=" N TYR R 192 " pdb=" CA TYR R 192 " ideal model delta sigma weight residual 122.17 116.39 5.78 1.54e+00 4.22e-01 1.41e+01 angle pdb=" C PHE R 27 " pdb=" N VAL R 28 " pdb=" CA VAL R 28 " ideal model delta sigma weight residual 120.24 122.30 -2.06 6.30e-01 2.52e+00 1.07e+01 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.56 114.56 -3.00 1.01e+00 9.80e-01 8.84e+00 ... (remaining 11497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4568 17.34 - 34.69: 384 34.69 - 52.03: 74 52.03 - 69.38: 8 69.38 - 86.72: 12 Dihedral angle restraints: 5046 sinusoidal: 1999 harmonic: 3047 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -29.67 -56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CA ASN R 168 " pdb=" C ASN R 168 " pdb=" N ILE R 169 " pdb=" CA ILE R 169 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TRP R 117 " pdb=" C TRP R 117 " pdb=" N ILE R 118 " pdb=" CA ILE R 118 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 798 0.033 - 0.065: 327 0.065 - 0.098: 115 0.098 - 0.130: 53 0.130 - 0.163: 6 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CA LYS A 283 " pdb=" N LYS A 283 " pdb=" C LYS A 283 " pdb=" CB LYS A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB ILE R 104 " pdb=" CA ILE R 104 " pdb=" CG1 ILE R 104 " pdb=" CG2 ILE R 104 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CG LEU A 46 " pdb=" CB LEU A 46 " pdb=" CD1 LEU A 46 " pdb=" CD2 LEU A 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1296 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 82 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C PHE R 82 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE R 82 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL R 83 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 141 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO R 142 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 142 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 142 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 87 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C LEU R 87 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU R 87 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU R 88 " -0.012 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 152 2.66 - 3.22: 8202 3.22 - 3.78: 13218 3.78 - 4.34: 18392 4.34 - 4.90: 29777 Nonbonded interactions: 69741 Sorted by model distance: nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.099 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.131 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.137 2.440 nonbonded pdb=" OD1 ASP A 249 " pdb=" NZ LYS A 283 " model vdw 2.163 2.520 nonbonded pdb=" OD2 ASP B 27 " pdb=" OG SER G 31 " model vdw 2.197 2.440 ... (remaining 69736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.660 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8482 Z= 0.240 Angle : 0.656 7.796 11502 Z= 0.364 Chirality : 0.044 0.163 1299 Planarity : 0.004 0.051 1459 Dihedral : 13.682 86.724 3070 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.87 (0.26), residues: 1030 helix: 0.32 (0.28), residues: 380 sheet: -2.64 (0.33), residues: 182 loop : -1.94 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.020 0.002 PHE R 79 TYR 0.015 0.001 TYR R 253 ARG 0.010 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6520 (t0) cc_final: 0.6168 (t0) REVERT: A 248 VAL cc_start: 0.8214 (p) cc_final: 0.7980 (m) REVERT: A 313 ASP cc_start: 0.7203 (p0) cc_final: 0.6800 (p0) REVERT: A 368 ASP cc_start: 0.6576 (m-30) cc_final: 0.6062 (m-30) REVERT: A 377 ASN cc_start: 0.7683 (m110) cc_final: 0.7413 (m-40) REVERT: B 277 SER cc_start: 0.7897 (p) cc_final: 0.7622 (p) REVERT: G 58 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7160 (mm-30) REVERT: R 141 TYR cc_start: 0.7993 (p90) cc_final: 0.7622 (p90) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2371 time to fit residues: 65.2605 Evaluate side-chains 201 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.0010 chunk 76 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 340 ASN G 59 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8482 Z= 0.214 Angle : 0.569 8.653 11502 Z= 0.298 Chirality : 0.043 0.152 1299 Planarity : 0.004 0.052 1459 Dihedral : 5.329 50.089 1155 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.55 % Allowed : 9.65 % Favored : 88.80 % 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: -1.50 (0.26), residues: 1030 helix: 0.57 (0.29), residues: 376 sheet: -2.10 (0.33), residues: 184 loop : -1.80 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 181 PHE 0.017 0.002 PHE A 330 TYR 0.017 0.001 TYR R 253 ARG 0.004 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 0.933 Fit side-chains REVERT: A 49 ASP cc_start: 0.6484 (t0) cc_final: 0.6143 (t0) REVERT: A 313 ASP cc_start: 0.7183 (p0) cc_final: 0.6876 (p0) REVERT: A 368 ASP cc_start: 0.6561 (m-30) cc_final: 0.6090 (m-30) REVERT: A 377 ASN cc_start: 0.7726 (m110) cc_final: 0.7375 (m-40) REVERT: B 277 SER cc_start: 0.7766 (p) cc_final: 0.7328 (t) REVERT: G 58 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7175 (mm-30) REVERT: R 247 MET cc_start: 0.4403 (ttm) cc_final: 0.2965 (mtt) outliers start: 14 outliers final: 13 residues processed: 212 average time/residue: 0.2255 time to fit residues: 64.0460 Evaluate side-chains 214 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 0.0070 chunk 62 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.0670 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 73 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8482 Z= 0.149 Angle : 0.526 5.722 11502 Z= 0.277 Chirality : 0.041 0.142 1299 Planarity : 0.004 0.052 1459 Dihedral : 5.030 46.475 1155 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.44 % Allowed : 13.53 % Favored : 84.04 % 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: -1.25 (0.26), residues: 1030 helix: 0.77 (0.29), residues: 372 sheet: -2.00 (0.33), residues: 179 loop : -1.63 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 181 PHE 0.017 0.001 PHE A 330 TYR 0.014 0.001 TYR R 32 ARG 0.006 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 0.850 Fit side-chains REVERT: A 11 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5816 (m-30) REVERT: A 49 ASP cc_start: 0.6468 (t0) cc_final: 0.6100 (t0) REVERT: A 229 ASP cc_start: 0.6984 (p0) cc_final: 0.6753 (p0) REVERT: A 313 ASP cc_start: 0.7225 (p0) cc_final: 0.6882 (p0) REVERT: A 330 PHE cc_start: 0.7370 (t80) cc_final: 0.7147 (t80) REVERT: A 368 ASP cc_start: 0.6582 (m-30) cc_final: 0.6094 (m-30) REVERT: B 156 GLN cc_start: 0.7663 (mt0) cc_final: 0.7359 (mt0) REVERT: B 277 SER cc_start: 0.7765 (p) cc_final: 0.7299 (t) REVERT: G 58 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7164 (mm-30) outliers start: 22 outliers final: 16 residues processed: 214 average time/residue: 0.2358 time to fit residues: 67.3057 Evaluate side-chains 220 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8482 Z= 0.247 Angle : 0.551 6.083 11502 Z= 0.290 Chirality : 0.043 0.191 1299 Planarity : 0.004 0.052 1459 Dihedral : 5.216 43.669 1155 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.44 % Allowed : 14.75 % Favored : 81.82 % 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: -1.33 (0.26), residues: 1030 helix: 0.66 (0.29), residues: 380 sheet: -1.88 (0.34), residues: 188 loop : -1.74 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 180 PHE 0.017 0.002 PHE R 282 TYR 0.016 0.001 TYR R 253 ARG 0.007 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6445 (t0) cc_final: 0.6079 (t0) REVERT: A 313 ASP cc_start: 0.7222 (p0) cc_final: 0.6857 (p0) REVERT: A 363 ARG cc_start: 0.7724 (tpp-160) cc_final: 0.7342 (tpp-160) REVERT: B 156 GLN cc_start: 0.7716 (mt0) cc_final: 0.7458 (mt0) REVERT: B 277 SER cc_start: 0.7711 (p) cc_final: 0.7254 (t) REVERT: G 58 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7103 (mm-30) REVERT: R 161 ILE cc_start: 0.7750 (mm) cc_final: 0.7504 (mt) outliers start: 31 outliers final: 21 residues processed: 220 average time/residue: 0.2296 time to fit residues: 66.4908 Evaluate side-chains 218 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8482 Z= 0.224 Angle : 0.560 6.841 11502 Z= 0.291 Chirality : 0.042 0.189 1299 Planarity : 0.004 0.053 1459 Dihedral : 5.368 47.949 1155 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.99 % Allowed : 17.41 % Favored : 79.60 % 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: -1.25 (0.26), residues: 1030 helix: 0.65 (0.28), residues: 387 sheet: -1.76 (0.33), residues: 201 loop : -1.66 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.029 0.002 PHE A 330 TYR 0.015 0.001 TYR R 253 ARG 0.007 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6450 (t0) cc_final: 0.6075 (t0) REVERT: A 256 LEU cc_start: 0.8214 (tt) cc_final: 0.7867 (tp) REVERT: A 313 ASP cc_start: 0.7195 (p0) cc_final: 0.6834 (p0) REVERT: A 363 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7393 (tpp-160) REVERT: A 377 ASN cc_start: 0.7776 (m110) cc_final: 0.7378 (m-40) REVERT: B 55 LEU cc_start: 0.7376 (mt) cc_final: 0.7139 (mp) REVERT: B 156 GLN cc_start: 0.7693 (mt0) cc_final: 0.7425 (mt0) REVERT: B 277 SER cc_start: 0.7699 (p) cc_final: 0.7242 (t) REVERT: G 58 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7082 (mm-30) REVERT: N 34 MET cc_start: 0.6874 (mmm) cc_final: 0.6380 (mtp) REVERT: R 161 ILE cc_start: 0.7748 (mm) cc_final: 0.7473 (mt) outliers start: 27 outliers final: 23 residues processed: 216 average time/residue: 0.2343 time to fit residues: 67.5441 Evaluate side-chains 223 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 247 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8482 Z= 0.307 Angle : 0.596 6.622 11502 Z= 0.312 Chirality : 0.044 0.186 1299 Planarity : 0.005 0.053 1459 Dihedral : 5.660 52.765 1155 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.88 % Allowed : 16.74 % Favored : 79.38 % 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: -1.28 (0.26), residues: 1030 helix: 0.72 (0.28), residues: 378 sheet: -1.74 (0.33), residues: 200 loop : -1.76 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 180 PHE 0.029 0.002 PHE A 330 TYR 0.016 0.002 TYR R 253 ARG 0.008 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 207 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6454 (t0) cc_final: 0.6145 (t0) REVERT: A 256 LEU cc_start: 0.8266 (tt) cc_final: 0.7885 (tp) REVERT: A 313 ASP cc_start: 0.7207 (p0) cc_final: 0.6854 (p0) REVERT: A 330 PHE cc_start: 0.7427 (t80) cc_final: 0.7209 (t80) REVERT: A 340 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7513 (p) REVERT: B 55 LEU cc_start: 0.7442 (mt) cc_final: 0.7177 (mp) REVERT: B 188 MET cc_start: 0.6270 (mtp) cc_final: 0.5870 (mtp) REVERT: B 277 SER cc_start: 0.7652 (p) cc_final: 0.7201 (t) REVERT: B 292 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: G 58 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7045 (mm-30) REVERT: R 266 MET cc_start: 0.4909 (ppp) cc_final: 0.4454 (ppp) REVERT: R 273 LEU cc_start: 0.7390 (mt) cc_final: 0.7136 (mt) outliers start: 35 outliers final: 30 residues processed: 222 average time/residue: 0.2344 time to fit residues: 68.8717 Evaluate side-chains 237 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 247 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.1980 chunk 71 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 251 HIS R 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8482 Z= 0.188 Angle : 0.553 7.642 11502 Z= 0.287 Chirality : 0.042 0.160 1299 Planarity : 0.004 0.053 1459 Dihedral : 5.454 57.306 1155 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.77 % Allowed : 19.18 % Favored : 77.05 % 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: -1.11 (0.26), residues: 1030 helix: 0.78 (0.28), residues: 381 sheet: -1.69 (0.33), residues: 200 loop : -1.57 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 347 PHE 0.020 0.001 PHE R 282 TYR 0.014 0.001 TYR R 253 ARG 0.007 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 206 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6436 (t0) cc_final: 0.6103 (t0) REVERT: A 256 LEU cc_start: 0.8194 (tt) cc_final: 0.7824 (tp) REVERT: A 313 ASP cc_start: 0.7183 (p0) cc_final: 0.6919 (p0) REVERT: A 330 PHE cc_start: 0.7413 (t80) cc_final: 0.6404 (t80) REVERT: A 334 GLU cc_start: 0.6430 (mt-10) cc_final: 0.6120 (mp0) REVERT: A 336 LEU cc_start: 0.7624 (mm) cc_final: 0.7276 (mt) REVERT: A 363 ARG cc_start: 0.7719 (tpp-160) cc_final: 0.7453 (tpp-160) REVERT: A 368 ASP cc_start: 0.6599 (m-30) cc_final: 0.6310 (t0) REVERT: A 377 ASN cc_start: 0.7806 (m110) cc_final: 0.7395 (m-40) REVERT: B 55 LEU cc_start: 0.7347 (mt) cc_final: 0.7024 (mp) REVERT: B 156 GLN cc_start: 0.7714 (mt0) cc_final: 0.7416 (mt0) REVERT: B 277 SER cc_start: 0.7652 (p) cc_final: 0.7207 (t) REVERT: R 266 MET cc_start: 0.4973 (ppp) cc_final: 0.4528 (ppp) outliers start: 34 outliers final: 29 residues processed: 219 average time/residue: 0.2300 time to fit residues: 66.9790 Evaluate side-chains 230 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 201 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 247 MET Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 85 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 HIS R 277 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8482 Z= 0.208 Angle : 0.558 7.612 11502 Z= 0.290 Chirality : 0.042 0.160 1299 Planarity : 0.004 0.053 1459 Dihedral : 5.521 52.221 1155 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.99 % Allowed : 18.96 % Favored : 77.05 % 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: -1.11 (0.26), residues: 1030 helix: 0.85 (0.29), residues: 372 sheet: -1.67 (0.33), residues: 201 loop : -1.60 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 251 PHE 0.024 0.001 PHE A 330 TYR 0.014 0.001 TYR R 253 ARG 0.008 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6365 (t0) cc_final: 0.6023 (t0) REVERT: A 256 LEU cc_start: 0.8250 (tt) cc_final: 0.7864 (tp) REVERT: A 313 ASP cc_start: 0.7191 (p0) cc_final: 0.6840 (p0) REVERT: A 330 PHE cc_start: 0.7461 (t80) cc_final: 0.7188 (t80) REVERT: A 363 ARG cc_start: 0.7725 (tpp-160) cc_final: 0.7422 (tpp-160) REVERT: A 368 ASP cc_start: 0.6607 (m-30) cc_final: 0.6312 (t0) REVERT: B 49 ARG cc_start: 0.7697 (mpt180) cc_final: 0.7475 (mpt180) REVERT: B 156 GLN cc_start: 0.7726 (mt0) cc_final: 0.7438 (mt0) REVERT: B 277 SER cc_start: 0.7621 (p) cc_final: 0.7209 (t) REVERT: B 292 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: N 31 ASN cc_start: 0.6401 (m110) cc_final: 0.6091 (m110) REVERT: R 48 VAL cc_start: 0.7138 (p) cc_final: 0.6880 (t) REVERT: R 266 MET cc_start: 0.4990 (ppp) cc_final: 0.4555 (ppp) outliers start: 36 outliers final: 28 residues processed: 216 average time/residue: 0.2308 time to fit residues: 66.3762 Evaluate side-chains 227 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 247 MET Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.0050 chunk 59 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8482 Z= 0.206 Angle : 0.573 9.355 11502 Z= 0.294 Chirality : 0.043 0.162 1299 Planarity : 0.004 0.053 1459 Dihedral : 5.471 48.965 1155 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.44 % Allowed : 19.51 % Favored : 77.05 % 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: -1.10 (0.26), residues: 1030 helix: 0.86 (0.28), residues: 375 sheet: -1.64 (0.34), residues: 199 loop : -1.62 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS R 251 PHE 0.024 0.001 PHE A 330 TYR 0.018 0.001 TYR R 253 ARG 0.007 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8253 (tt) cc_final: 0.7868 (tp) REVERT: A 313 ASP cc_start: 0.7191 (p0) cc_final: 0.6837 (p0) REVERT: A 330 PHE cc_start: 0.7463 (t80) cc_final: 0.6722 (t80) REVERT: A 336 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7239 (mt) REVERT: A 363 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7411 (tpp-160) REVERT: A 368 ASP cc_start: 0.6588 (m-30) cc_final: 0.6282 (t0) REVERT: A 377 ASN cc_start: 0.7805 (m110) cc_final: 0.7383 (m-40) REVERT: B 156 GLN cc_start: 0.7707 (mt0) cc_final: 0.7403 (mt0) REVERT: B 188 MET cc_start: 0.6189 (mtp) cc_final: 0.5914 (mtp) REVERT: B 277 SER cc_start: 0.7613 (p) cc_final: 0.7204 (t) REVERT: B 292 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: N 31 ASN cc_start: 0.6365 (m110) cc_final: 0.6066 (m110) REVERT: R 48 VAL cc_start: 0.7142 (p) cc_final: 0.6885 (t) outliers start: 31 outliers final: 27 residues processed: 216 average time/residue: 0.2291 time to fit residues: 66.1209 Evaluate side-chains 230 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 201 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 247 MET Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 92 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN R 251 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8482 Z= 0.206 Angle : 0.577 7.089 11502 Z= 0.297 Chirality : 0.043 0.162 1299 Planarity : 0.004 0.053 1459 Dihedral : 5.408 44.901 1155 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.22 % Allowed : 19.51 % Favored : 77.27 % 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: -1.08 (0.26), residues: 1030 helix: 0.79 (0.28), residues: 379 sheet: -1.63 (0.34), residues: 199 loop : -1.55 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 251 PHE 0.027 0.001 PHE A 330 TYR 0.018 0.001 TYR R 253 ARG 0.008 0.000 ARG A 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8246 (tt) cc_final: 0.7882 (tp) REVERT: A 313 ASP cc_start: 0.7186 (p0) cc_final: 0.6854 (p0) REVERT: A 330 PHE cc_start: 0.7295 (t80) cc_final: 0.6498 (t80) REVERT: A 334 GLU cc_start: 0.6588 (mp0) cc_final: 0.6188 (mp0) REVERT: A 363 ARG cc_start: 0.7720 (tpp-160) cc_final: 0.7416 (tpp-160) REVERT: A 368 ASP cc_start: 0.6599 (m-30) cc_final: 0.6311 (t0) REVERT: A 377 ASN cc_start: 0.7821 (m110) cc_final: 0.7397 (m-40) REVERT: B 156 GLN cc_start: 0.7703 (mt0) cc_final: 0.7422 (mt0) REVERT: B 188 MET cc_start: 0.6182 (mtp) cc_final: 0.5939 (mtp) REVERT: B 277 SER cc_start: 0.7594 (p) cc_final: 0.7194 (t) REVERT: B 292 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6697 (m-80) REVERT: N 31 ASN cc_start: 0.6381 (m110) cc_final: 0.6087 (m110) REVERT: R 48 VAL cc_start: 0.7150 (p) cc_final: 0.6885 (t) REVERT: R 148 VAL cc_start: 0.6977 (m) cc_final: 0.6733 (p) REVERT: R 266 MET cc_start: 0.5033 (ppp) cc_final: 0.4617 (ppp) outliers start: 29 outliers final: 27 residues processed: 209 average time/residue: 0.2333 time to fit residues: 64.4569 Evaluate side-chains 224 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 196 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 247 MET Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.0060 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.160829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145015 restraints weight = 11613.791| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.87 r_work: 0.3661 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8482 Z= 0.193 Angle : 0.577 6.949 11502 Z= 0.294 Chirality : 0.043 0.159 1299 Planarity : 0.004 0.053 1459 Dihedral : 5.323 41.391 1155 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.66 % Allowed : 19.07 % Favored : 77.27 % 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: -1.05 (0.26), residues: 1030 helix: 0.80 (0.28), residues: 379 sheet: -1.61 (0.34), residues: 199 loop : -1.53 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 251 PHE 0.024 0.001 PHE A 330 TYR 0.016 0.001 TYR R 253 ARG 0.007 0.000 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2350.57 seconds wall clock time: 43 minutes 23.08 seconds (2603.08 seconds total)