Starting phenix.real_space_refine on Tue Nov 14 19:06:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/11_2023/7vuh_32128_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/11_2023/7vuh_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_32128/11_2023/7vuh_32128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/11_2023/7vuh_32128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/11_2023/7vuh_32128_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuh_32128/11_2023/7vuh_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-1.21rc1-5144/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: 5.01, per 1000 atoms: 0.60 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 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: 1.70 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: 2.10 Time building geometry restraints manager: 3.46 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: 68 52.03 - 69.38: 8 69.38 - 86.72: 12 Dihedral angle restraints: 5040 sinusoidal: 1993 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 5037 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: 0.850 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: 3.810 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.100 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- 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 : 13.587 86.724 3064 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 *********************** 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 : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2659 time to fit residues: 73.0249 Evaluate side-chains 201 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3299 ------------------------------------------------------------------------------- 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: 0.0000 chunk 76 optimal weight: 0.6980 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: 0.5984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8482 Z= 0.242 Angle : 0.584 8.522 11502 Z= 0.306 Chirality : 0.044 0.156 1299 Planarity : 0.004 0.052 1459 Dihedral : 4.935 48.365 1149 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.88 % Allowed : 9.87 % Favored : 88.25 % 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: -1.52 (0.26), residues: 1030 helix: 0.56 (0.29), residues: 375 sheet: -2.10 (0.33), residues: 186 loop : -1.82 (0.28), residues: 469 *********************** 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 231 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 214 time to evaluate : 0.900 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 220 average time/residue: 0.2213 time to fit residues: 65.1240 Evaluate side-chains 216 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0792 time to fit residues: 3.1601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 0.0040 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8482 Z= 0.220 Angle : 0.565 8.760 11502 Z= 0.296 Chirality : 0.043 0.189 1299 Planarity : 0.005 0.052 1459 Dihedral : 4.872 46.328 1149 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.66 % Allowed : 14.08 % Favored : 84.26 % 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: -1.37 (0.26), residues: 1030 helix: 0.67 (0.29), residues: 374 sheet: -1.98 (0.33), residues: 188 loop : -1.72 (0.28), residues: 468 *********************** 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 223 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 1.183 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 212 average time/residue: 0.2286 time to fit residues: 64.2101 Evaluate side-chains 207 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 199 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1161 time to fit residues: 2.8169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8482 Z= 0.271 Angle : 0.585 7.513 11502 Z= 0.306 Chirality : 0.043 0.158 1299 Planarity : 0.004 0.052 1459 Dihedral : 5.004 36.503 1149 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.55 % Allowed : 16.30 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.26), residues: 1030 helix: 0.64 (0.28), residues: 378 sheet: -1.88 (0.33), residues: 197 loop : -1.76 (0.28), residues: 455 *********************** 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 228 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.885 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 215 average time/residue: 0.2295 time to fit residues: 65.4999 Evaluate side-chains 209 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0829 time to fit residues: 3.0143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6739 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8482 Z= 0.230 Angle : 0.579 8.665 11502 Z= 0.299 Chirality : 0.043 0.186 1299 Planarity : 0.004 0.052 1459 Dihedral : 4.924 37.450 1149 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.77 % Allowed : 17.96 % Favored : 80.27 % 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: -1.30 (0.26), residues: 1030 helix: 0.71 (0.28), residues: 378 sheet: -1.77 (0.34), residues: 200 loop : -1.77 (0.28), residues: 452 *********************** 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 211 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 0.915 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 201 average time/residue: 0.2279 time to fit residues: 60.6702 Evaluate side-chains 197 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1124 time to fit residues: 2.7617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6731 moved from start: 0.1878 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= 0.210 Angle : 0.568 9.964 11502 Z= 0.293 Chirality : 0.043 0.162 1299 Planarity : 0.004 0.053 1459 Dihedral : 4.868 37.506 1149 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.44 % Allowed : 18.96 % 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: -1.21 (0.26), residues: 1030 helix: 0.75 (0.28), residues: 381 sheet: -1.69 (0.33), residues: 208 loop : -1.69 (0.29), residues: 441 *********************** 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 208 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 0.912 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 203 average time/residue: 0.2328 time to fit residues: 62.4677 Evaluate side-chains 202 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0816 time to fit residues: 2.0418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.0170 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6716 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8482 Z= 0.193 Angle : 0.578 9.117 11502 Z= 0.297 Chirality : 0.042 0.174 1299 Planarity : 0.004 0.053 1459 Dihedral : 4.821 36.507 1149 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.89 % Allowed : 20.07 % Favored : 79.05 % 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: -1.13 (0.26), residues: 1030 helix: 0.76 (0.28), residues: 383 sheet: -1.66 (0.34), residues: 197 loop : -1.62 (0.29), residues: 450 *********************** 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 213 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 205 time to evaluate : 0.946 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 209 average time/residue: 0.2341 time to fit residues: 64.7304 Evaluate side-chains 205 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0792 time to fit residues: 2.3549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.0040 chunk 48 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8482 Z= 0.194 Angle : 0.588 14.590 11502 Z= 0.299 Chirality : 0.043 0.161 1299 Planarity : 0.004 0.054 1459 Dihedral : 4.817 36.419 1149 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.78 % Allowed : 20.62 % Favored : 78.60 % 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: -1.11 (0.26), residues: 1030 helix: 0.88 (0.28), residues: 373 sheet: -1.62 (0.34), residues: 197 loop : -1.67 (0.28), residues: 460 *********************** 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 206 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 0.907 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 203 average time/residue: 0.2484 time to fit residues: 66.1190 Evaluate side-chains 197 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0784 time to fit residues: 1.7461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 54 optimal weight: 0.0970 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8482 Z= 0.205 Angle : 0.598 13.889 11502 Z= 0.304 Chirality : 0.042 0.157 1299 Planarity : 0.004 0.054 1459 Dihedral : 4.881 36.984 1149 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.78 % Allowed : 21.51 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1030 helix: 0.73 (0.28), residues: 381 sheet: -1.54 (0.34), residues: 197 loop : -1.64 (0.28), residues: 452 *********************** 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 204 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 197 time to evaluate : 0.853 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 201 average time/residue: 0.2408 time to fit residues: 63.2945 Evaluate side-chains 201 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0829 time to fit residues: 1.9176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8482 Z= 0.334 Angle : 0.671 16.104 11502 Z= 0.344 Chirality : 0.046 0.197 1299 Planarity : 0.005 0.054 1459 Dihedral : 5.299 39.791 1149 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.22 % Allowed : 21.51 % Favored : 78.27 % 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: -1.30 (0.26), residues: 1030 helix: 0.50 (0.28), residues: 390 sheet: -1.58 (0.34), residues: 203 loop : -1.71 (0.29), residues: 437 ********************** 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 203 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 0.914 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 201 average time/residue: 0.2425 time to fit residues: 64.2437 Evaluate side-chains 194 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0795 time to fit residues: 1.5581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.156232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.140738 restraints weight = 11707.752| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.81 r_work: 0.3656 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8482 Z= 0.298 Angle : 0.665 15.111 11502 Z= 0.339 Chirality : 0.045 0.170 1299 Planarity : 0.005 0.055 1459 Dihedral : 5.278 38.856 1149 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.11 % Allowed : 22.73 % Favored : 77.16 % 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: 0.53 (0.28), residues: 389 sheet: -1.67 (0.34), residues: 201 loop : -1.65 (0.29), residues: 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.13 seconds wall clock time: 42 minutes 5.47 seconds (2525.47 seconds total)