Starting phenix.real_space_refine on Wed Feb 14 14:29:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fro_29403/02_2024/8fro_29403_updated.pdb" } resolution = 3.25 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= 0.005 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 Cl 2 4.86 5 C 5950 2.51 5 N 1554 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9170 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "F" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2525 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 2712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2712 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 12, 'TRANS': 325} Chain breaks: 2 Chain: "F" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 188 Unusual residues: {'JSG': 1, 'MG3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'JSG:plan-7': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.11, per 1000 atoms: 0.56 Number of scatterers: 9170 At special positions: 0 Unit cell: (71.38, 128.65, 104.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 40 16.00 P 2 15.00 O 1622 8.00 N 1554 7.00 C 5950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.82 Conformation dependent library (CDL) restraints added in 1.6 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 10 sheets defined 54.1% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.795A pdb=" N ILE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 148 through 162 removed outlier: 3.889A pdb=" N ALA A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.159A pdb=" N GLY A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 removed outlier: 3.572A pdb=" N ALA A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.796A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 133 Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 162 removed outlier: 3.888A pdb=" N ALA B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.159A pdb=" N GLY B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.573A pdb=" N ALA B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'F' and resid 3 through 40 Processing helix chain 'F' and resid 48 through 81 Proline residue: F 57 - end of helix removed outlier: 3.908A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 84 through 90 Processing helix chain 'F' and resid 95 through 118 removed outlier: 3.579A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 104 - end of helix Processing helix chain 'F' and resid 120 through 137 removed outlier: 4.038A pdb=" N VAL F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 143 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 253 through 256 No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 263 through 289 Proline residue: F 276 - end of helix removed outlier: 4.650A pdb=" N ILE F 279 " --> pdb=" O GLY F 275 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL F 280 " --> pdb=" O PRO F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 325 removed outlier: 3.750A pdb=" N THR F 321 " --> pdb=" O ILE F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 349 Proline residue: F 334 - end of helix removed outlier: 4.081A pdb=" N ILE F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA F 343 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU F 346 " --> pdb=" O ALA F 343 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER F 348 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 39 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 59 through 84 Proline residue: G 68 - end of helix Processing helix chain 'G' and resid 87 through 93 Processing helix chain 'G' and resid 98 through 122 removed outlier: 4.075A pdb=" N VAL G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 136 removed outlier: 3.635A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 236 through 239 removed outlier: 3.612A pdb=" N THR G 239 " --> pdb=" O HIS G 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 236 through 239' Processing helix chain 'G' and resid 247 through 260 Processing helix chain 'G' and resid 265 through 275 Processing helix chain 'G' and resid 277 through 293 Processing helix chain 'G' and resid 301 through 328 Processing helix chain 'G' and resid 333 through 353 Proline residue: G 340 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 32 through 35 Processing sheet with id= B, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.787A pdb=" N ILE A 217 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A 226 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 215 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A 198 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU A 42 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 200 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 17 through 19 removed outlier: 7.495A pdb=" N LYS A 19 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS A 28 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 32 through 35 Processing sheet with id= E, first strand: chain 'B' and resid 222 through 227 removed outlier: 6.786A pdb=" N ILE B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 226 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA B 215 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 198 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 42 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 200 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 17 through 19 removed outlier: 7.496A pdb=" N LYS B 19 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS B 28 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 148 through 152 removed outlier: 4.228A pdb=" N GLU F 148 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 159 " --> pdb=" O GLU F 148 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER F 224 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 192 through 194 removed outlier: 3.586A pdb=" N VAL F 206 " --> pdb=" O LEU F 233 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 149 through 153 Processing sheet with id= J, first strand: chain 'G' and resid 162 through 164 removed outlier: 4.050A pdb=" N GLN G 191 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLN G 199 " --> pdb=" O VAL G 195 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1410 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: 2.81 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2266 1.33 - 1.45: 1693 1.45 - 1.57: 5309 1.57 - 1.69: 2 1.69 - 1.81: 76 Bond restraints: 9346 Sorted by residual: bond pdb=" C7 JSG F 401 " pdb=" N2 JSG F 401 " ideal model delta sigma weight residual 1.621 1.330 0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C03 MG3 F 402 " pdb=" N02 MG3 F 402 " ideal model delta sigma weight residual 1.595 1.350 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C11 MG3 F 402 " pdb=" N10 MG3 F 402 " ideal model delta sigma weight residual 1.540 1.336 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" CDO JSG F 401 " pdb=" NAO JSG F 401 " ideal model delta sigma weight residual 1.505 1.329 0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C36 MG3 F 402 " pdb=" N35 MG3 F 402 " ideal model delta sigma weight residual 1.477 1.331 0.146 2.00e-02 2.50e+03 5.34e+01 ... (remaining 9341 not shown) Histogram of bond angle deviations from ideal: 98.25 - 105.47: 149 105.47 - 112.70: 4977 112.70 - 119.92: 3255 119.92 - 127.15: 4151 127.15 - 134.37: 87 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C12 MG3 F 402 " pdb=" N17 MG3 F 402 " pdb=" C18 MG3 F 402 " ideal model delta sigma weight residual 132.10 116.93 15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" C38 MG3 F 402 " pdb=" C39 MG3 F 402 " pdb=" C40 MG3 F 402 " ideal model delta sigma weight residual 112.64 127.43 -14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C38 MG3 F 402 " pdb=" C39 MG3 F 402 " pdb=" C47 MG3 F 402 " ideal model delta sigma weight residual 139.33 126.34 12.99 3.00e+00 1.11e-01 1.88e+01 angle pdb=" C34 MG3 F 402 " pdb=" N35 MG3 F 402 " pdb=" C36 MG3 F 402 " ideal model delta sigma weight residual 109.47 121.82 -12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C04 MG3 F 402 " pdb=" N10 MG3 F 402 " pdb=" C11 MG3 F 402 " ideal model delta sigma weight residual 110.01 121.58 -11.57 3.00e+00 1.11e-01 1.49e+01 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 5482 35.93 - 71.86: 95 71.86 - 107.79: 16 107.79 - 143.72: 2 143.72 - 179.65: 3 Dihedral angle restraints: 5598 sinusoidal: 2333 harmonic: 3265 Sorted by residual: dihedral pdb=" N02 MG3 F 402 " pdb=" C36 MG3 F 402 " pdb=" C37 MG3 F 402 " pdb=" N35 MG3 F 402 " ideal model delta sinusoidal sigma weight residual 113.69 -66.66 -179.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N10 MG3 F 402 " pdb=" C11 MG3 F 402 " pdb=" C12 MG3 F 402 " pdb=" N17 MG3 F 402 " ideal model delta sinusoidal sigma weight residual -92.95 72.84 -165.79 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C26 MG3 F 402 " pdb=" C27 MG3 F 402 " pdb=" C34 MG3 F 402 " pdb=" N35 MG3 F 402 " ideal model delta sinusoidal sigma weight residual 86.47 -76.46 162.93 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1225 0.065 - 0.130: 190 0.130 - 0.195: 15 0.195 - 0.260: 2 0.260 - 0.325: 1 Chirality restraints: 1433 Sorted by residual: chirality pdb=" C12 MG3 F 402 " pdb=" C11 MG3 F 402 " pdb=" C13 MG3 F 402 " pdb=" N17 MG3 F 402 " both_signs ideal model delta sigma weight residual False 2.66 2.33 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CAN JSG F 401 " pdb=" CAL JSG F 401 " pdb=" CAP JSG F 401 " pdb=" NAO JSG F 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.75 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C2 JSG F 401 " pdb=" C1 JSG F 401 " pdb=" C3 JSG F 401 " pdb=" N2 JSG F 401 " both_signs ideal model delta sigma weight residual False -2.57 -2.78 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1430 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 MG3 F 402 " -0.017 2.00e-02 2.50e+03 4.03e-02 4.05e+01 pdb=" C27 MG3 F 402 " -0.001 2.00e-02 2.50e+03 pdb=" C28 MG3 F 402 " 0.019 2.00e-02 2.50e+03 pdb=" C30 MG3 F 402 " 0.023 2.00e-02 2.50e+03 pdb=" C31 MG3 F 402 " 0.005 2.00e-02 2.50e+03 pdb=" C32 MG3 F 402 " -0.017 2.00e-02 2.50e+03 pdb=" C34 MG3 F 402 " -0.073 2.00e-02 2.50e+03 pdb=" S25 MG3 F 402 " 0.087 2.00e-02 2.50e+03 pdb="CL29 MG3 F 402 " 0.014 2.00e-02 2.50e+03 pdb="CL33 MG3 F 402 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 MG3 F 402 " 0.035 2.00e-02 2.50e+03 3.00e-02 1.35e+01 pdb=" C03 MG3 F 402 " -0.003 2.00e-02 2.50e+03 pdb=" C04 MG3 F 402 " 0.038 2.00e-02 2.50e+03 pdb=" C37 MG3 F 402 " -0.036 2.00e-02 2.50e+03 pdb=" N02 MG3 F 402 " 0.004 2.00e-02 2.50e+03 pdb=" O50 MG3 F 402 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 245 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASP A 245 " 0.062 2.00e-02 2.50e+03 pdb=" O ASP A 245 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 246 " -0.021 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 2 2.12 - 2.81: 2466 2.81 - 3.51: 12871 3.51 - 4.20: 20759 4.20 - 4.90: 38321 Nonbonded interactions: 74419 Sorted by model distance: nonbonded pdb=" CBE JSG F 401 " pdb=" OBU JSG F 401 " model vdw 1.424 3.470 nonbonded pdb=" CBC JSG F 401 " pdb=" OBS JSG F 401 " model vdw 1.425 3.470 nonbonded pdb=" OD1 ASP F 161 " pdb=" N LEU F 162 " model vdw 2.275 2.520 nonbonded pdb=" O ILE F 308 " pdb=" OG SER F 311 " model vdw 2.282 2.440 nonbonded pdb=" OE1 GLN F 210 " pdb=" OE1 GLN F 229 " model vdw 2.305 3.040 ... (remaining 74414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 247) selection = chain 'B' } 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.009 0.291 9346 Z= 0.556 Angle : 0.762 15.166 12619 Z= 0.361 Chirality : 0.046 0.325 1433 Planarity : 0.005 0.076 1569 Dihedral : 15.551 179.651 3498 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.10 % Allowed : 0.42 % Favored : 99.48 % 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: 1.40 (0.25), residues: 1111 helix: 1.68 (0.22), residues: 590 sheet: 0.56 (0.40), residues: 153 loop : -0.03 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 200 HIS 0.001 0.000 HIS G 10 PHE 0.016 0.001 PHE G 226 TYR 0.016 0.001 TYR F 333 ARG 0.007 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7488 (pt0) cc_final: 0.7153 (pt0) REVERT: A 204 ASN cc_start: 0.8754 (t0) cc_final: 0.8527 (t0) REVERT: B 15 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7733 (mmtp) REVERT: B 33 GLU cc_start: 0.8110 (pt0) cc_final: 0.7904 (pt0) REVERT: B 213 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7622 (mt-10) REVERT: B 239 ARG cc_start: 0.7643 (mmt90) cc_final: 0.7332 (mmt180) REVERT: F 117 MET cc_start: 0.8401 (tpp) cc_final: 0.8101 (mmm) REVERT: F 147 LYS cc_start: 0.7950 (mttp) cc_final: 0.7453 (mttm) REVERT: F 194 THR cc_start: 0.8692 (t) cc_final: 0.8314 (p) REVERT: G 208 MET cc_start: 0.7549 (tmm) cc_final: 0.7017 (tmm) REVERT: G 344 MET cc_start: 0.7584 (mtm) cc_final: 0.7258 (mtt) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2540 time to fit residues: 59.2967 Evaluate side-chains 135 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9346 Z= 0.235 Angle : 0.553 7.179 12619 Z= 0.278 Chirality : 0.042 0.148 1433 Planarity : 0.004 0.061 1569 Dihedral : 13.177 171.922 1355 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.42 % Allowed : 4.80 % Favored : 94.79 % 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: 1.56 (0.25), residues: 1111 helix: 1.76 (0.21), residues: 602 sheet: 1.15 (0.42), residues: 141 loop : -0.16 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 271 HIS 0.004 0.001 HIS A 81 PHE 0.013 0.001 PHE G 226 TYR 0.012 0.001 TYR F 231 ARG 0.004 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.069 Fit side-chains REVERT: A 33 GLU cc_start: 0.7521 (pt0) cc_final: 0.7183 (pt0) REVERT: B 239 ARG cc_start: 0.7672 (mmt90) cc_final: 0.7384 (mmt180) REVERT: F 147 LYS cc_start: 0.8012 (mttp) cc_final: 0.7514 (mttm) REVERT: F 194 THR cc_start: 0.8698 (t) cc_final: 0.8337 (p) REVERT: F 212 ARG cc_start: 0.6808 (mtt90) cc_final: 0.6203 (mtp85) REVERT: F 326 ASP cc_start: 0.8816 (t0) cc_final: 0.8538 (t0) REVERT: G 208 MET cc_start: 0.7596 (tmm) cc_final: 0.7050 (tmm) REVERT: G 344 MET cc_start: 0.7645 (mtm) cc_final: 0.7383 (mtt) outliers start: 4 outliers final: 2 residues processed: 138 average time/residue: 0.2592 time to fit residues: 48.5636 Evaluate side-chains 134 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 76 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 121 GLN A 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9346 Z= 0.239 Angle : 0.535 7.011 12619 Z= 0.271 Chirality : 0.042 0.147 1433 Planarity : 0.004 0.054 1569 Dihedral : 12.926 165.956 1355 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.52 % Allowed : 6.78 % Favored : 92.70 % 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: 1.60 (0.25), residues: 1111 helix: 1.88 (0.21), residues: 596 sheet: 1.14 (0.41), residues: 143 loop : -0.27 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 200 HIS 0.003 0.001 HIS A 81 PHE 0.010 0.001 PHE F 173 TYR 0.013 0.001 TYR F 333 ARG 0.005 0.000 ARG G 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 1.064 Fit side-chains REVERT: A 33 GLU cc_start: 0.7590 (pt0) cc_final: 0.7203 (pt0) REVERT: B 239 ARG cc_start: 0.7641 (mmt90) cc_final: 0.7352 (mmt180) REVERT: F 147 LYS cc_start: 0.8014 (mttp) cc_final: 0.7528 (mttm) REVERT: F 212 ARG cc_start: 0.6808 (mtt90) cc_final: 0.6198 (mtp85) REVERT: F 213 ARG cc_start: 0.7065 (ttt-90) cc_final: 0.6619 (ttm-80) REVERT: F 326 ASP cc_start: 0.8801 (t0) cc_final: 0.8508 (t0) REVERT: G 208 MET cc_start: 0.7706 (tmm) cc_final: 0.7141 (tmm) REVERT: G 344 MET cc_start: 0.7658 (mtm) cc_final: 0.7421 (mtt) outliers start: 5 outliers final: 5 residues processed: 140 average time/residue: 0.2551 time to fit residues: 47.5267 Evaluate side-chains 142 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 0.0030 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9346 Z= 0.242 Angle : 0.524 6.913 12619 Z= 0.266 Chirality : 0.041 0.133 1433 Planarity : 0.004 0.049 1569 Dihedral : 12.762 162.013 1355 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.94 % Allowed : 8.76 % Favored : 90.30 % 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: 1.57 (0.25), residues: 1111 helix: 1.83 (0.21), residues: 602 sheet: 1.15 (0.41), residues: 143 loop : -0.28 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 200 HIS 0.003 0.001 HIS A 81 PHE 0.010 0.001 PHE G 194 TYR 0.017 0.001 TYR G 260 ARG 0.004 0.000 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.005 Fit side-chains REVERT: A 33 GLU cc_start: 0.7569 (pt0) cc_final: 0.7202 (pt0) REVERT: B 239 ARG cc_start: 0.7634 (mmt90) cc_final: 0.7304 (mmt180) REVERT: F 147 LYS cc_start: 0.8015 (mttp) cc_final: 0.7525 (mttm) REVERT: F 194 THR cc_start: 0.8490 (t) cc_final: 0.8077 (p) REVERT: F 212 ARG cc_start: 0.6776 (mtt90) cc_final: 0.6372 (mtt180) REVERT: F 213 ARG cc_start: 0.7074 (ttt-90) cc_final: 0.6693 (ttm-80) REVERT: F 326 ASP cc_start: 0.8927 (t0) cc_final: 0.8577 (t0) REVERT: G 208 MET cc_start: 0.7699 (tmm) cc_final: 0.7140 (tmm) REVERT: G 344 MET cc_start: 0.7670 (mtm) cc_final: 0.7451 (mtt) outliers start: 9 outliers final: 7 residues processed: 140 average time/residue: 0.2370 time to fit residues: 44.8964 Evaluate side-chains 140 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 90 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9346 Z= 0.169 Angle : 0.495 5.968 12619 Z= 0.252 Chirality : 0.040 0.161 1433 Planarity : 0.004 0.045 1569 Dihedral : 12.586 160.113 1355 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.83 % Allowed : 9.49 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1111 helix: 1.93 (0.21), residues: 602 sheet: 1.25 (0.42), residues: 143 loop : -0.27 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 271 HIS 0.002 0.000 HIS A 81 PHE 0.012 0.001 PHE G 194 TYR 0.014 0.001 TYR G 260 ARG 0.005 0.000 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.983 Fit side-chains REVERT: A 33 GLU cc_start: 0.7584 (pt0) cc_final: 0.7217 (pt0) REVERT: A 239 ARG cc_start: 0.8215 (mmt90) cc_final: 0.7945 (mmm-85) REVERT: B 239 ARG cc_start: 0.7608 (mmt90) cc_final: 0.7229 (mmt180) REVERT: F 117 MET cc_start: 0.8280 (tpp) cc_final: 0.8045 (mtt) REVERT: F 147 LYS cc_start: 0.8004 (mttp) cc_final: 0.7538 (mttm) REVERT: F 212 ARG cc_start: 0.6786 (mtt90) cc_final: 0.6128 (mtp85) REVERT: F 213 ARG cc_start: 0.7076 (ttt-90) cc_final: 0.6700 (ttm-80) REVERT: F 321 THR cc_start: 0.8988 (m) cc_final: 0.8642 (p) REVERT: F 326 ASP cc_start: 0.8917 (t0) cc_final: 0.8571 (t0) REVERT: G 208 MET cc_start: 0.7698 (tmm) cc_final: 0.7135 (tmm) outliers start: 8 outliers final: 4 residues processed: 143 average time/residue: 0.2250 time to fit residues: 44.2393 Evaluate side-chains 136 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 156 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 203 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9346 Z= 0.339 Angle : 0.572 7.782 12619 Z= 0.290 Chirality : 0.043 0.186 1433 Planarity : 0.004 0.042 1569 Dihedral : 12.706 158.816 1355 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.67 % Allowed : 9.91 % Favored : 88.43 % 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: 1.40 (0.25), residues: 1111 helix: 1.64 (0.21), residues: 603 sheet: 1.16 (0.42), residues: 143 loop : -0.30 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS A 81 PHE 0.011 0.001 PHE G 194 TYR 0.016 0.001 TYR G 260 ARG 0.006 0.000 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.015 Fit side-chains REVERT: A 33 GLU cc_start: 0.7598 (pt0) cc_final: 0.7334 (pt0) REVERT: A 239 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7929 (mmm-85) REVERT: B 131 ASN cc_start: 0.8307 (t0) cc_final: 0.8044 (t0) REVERT: B 239 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7202 (mmt180) REVERT: F 147 LYS cc_start: 0.8050 (mttp) cc_final: 0.7567 (mttm) REVERT: F 212 ARG cc_start: 0.6824 (mtt90) cc_final: 0.6140 (mtp85) REVERT: F 213 ARG cc_start: 0.7071 (ttt-90) cc_final: 0.6664 (ttm-80) REVERT: F 269 MET cc_start: 0.9031 (tpp) cc_final: 0.8484 (tpt) REVERT: F 326 ASP cc_start: 0.8932 (t0) cc_final: 0.8593 (t0) REVERT: G 208 MET cc_start: 0.7725 (tmm) cc_final: 0.7167 (tmm) outliers start: 16 outliers final: 10 residues processed: 146 average time/residue: 0.2268 time to fit residues: 45.2975 Evaluate side-chains 141 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 23 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS F 135 GLN ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9346 Z= 0.394 Angle : 0.595 8.112 12619 Z= 0.302 Chirality : 0.044 0.152 1433 Planarity : 0.004 0.040 1569 Dihedral : 12.874 158.049 1355 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 10.84 % Favored : 87.70 % 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: 1.03 (0.25), residues: 1111 helix: 1.31 (0.21), residues: 608 sheet: 0.91 (0.43), residues: 137 loop : -0.38 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS A 81 PHE 0.013 0.001 PHE G 194 TYR 0.011 0.001 TYR G 260 ARG 0.008 0.000 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.332 Fit side-chains REVERT: A 33 GLU cc_start: 0.7612 (pt0) cc_final: 0.7330 (pt0) REVERT: A 62 ARG cc_start: 0.7616 (ttt180) cc_final: 0.7412 (ttt180) REVERT: A 239 ARG cc_start: 0.8254 (mmt90) cc_final: 0.7951 (mmm-85) REVERT: B 131 ASN cc_start: 0.8405 (t0) cc_final: 0.8072 (t0) REVERT: B 213 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7554 (mt-10) REVERT: F 147 LYS cc_start: 0.8066 (mttp) cc_final: 0.7570 (mttm) REVERT: F 212 ARG cc_start: 0.6853 (mtt90) cc_final: 0.6076 (mtt90) REVERT: F 326 ASP cc_start: 0.8933 (t0) cc_final: 0.8607 (t0) REVERT: G 208 MET cc_start: 0.7722 (tmm) cc_final: 0.7182 (tmm) outliers start: 14 outliers final: 14 residues processed: 150 average time/residue: 0.2614 time to fit residues: 52.3318 Evaluate side-chains 142 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9346 Z= 0.216 Angle : 0.523 6.534 12619 Z= 0.267 Chirality : 0.041 0.172 1433 Planarity : 0.004 0.041 1569 Dihedral : 12.734 157.028 1355 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.15 % Allowed : 11.68 % Favored : 87.17 % 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: 1.24 (0.26), residues: 1111 helix: 1.55 (0.21), residues: 607 sheet: 0.93 (0.43), residues: 137 loop : -0.37 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 271 HIS 0.002 0.001 HIS A 81 PHE 0.013 0.001 PHE G 194 TYR 0.015 0.001 TYR G 260 ARG 0.004 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.984 Fit side-chains REVERT: A 33 GLU cc_start: 0.7589 (pt0) cc_final: 0.7316 (pt0) REVERT: A 239 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7921 (mmm-85) REVERT: B 131 ASN cc_start: 0.8345 (t0) cc_final: 0.8074 (t0) REVERT: B 239 ARG cc_start: 0.7706 (tpp80) cc_final: 0.7108 (mmt180) REVERT: F 147 LYS cc_start: 0.8056 (mttp) cc_final: 0.7570 (mttm) REVERT: F 212 ARG cc_start: 0.6878 (mtt90) cc_final: 0.6140 (mtp85) REVERT: F 326 ASP cc_start: 0.8941 (t0) cc_final: 0.8598 (t0) REVERT: G 208 MET cc_start: 0.7761 (tmm) cc_final: 0.7227 (tmm) outliers start: 11 outliers final: 10 residues processed: 134 average time/residue: 0.2327 time to fit residues: 42.7641 Evaluate side-chains 134 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9346 Z= 0.263 Angle : 0.540 7.132 12619 Z= 0.274 Chirality : 0.042 0.184 1433 Planarity : 0.004 0.041 1569 Dihedral : 12.735 156.982 1355 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.36 % Allowed : 12.20 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1111 helix: 1.52 (0.21), residues: 607 sheet: 0.90 (0.44), residues: 137 loop : -0.38 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 271 HIS 0.003 0.001 HIS A 81 PHE 0.013 0.001 PHE G 194 TYR 0.017 0.001 TYR G 260 ARG 0.005 0.000 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.094 Fit side-chains REVERT: A 33 GLU cc_start: 0.7618 (pt0) cc_final: 0.7332 (pt0) REVERT: A 62 ARG cc_start: 0.7547 (ttt180) cc_final: 0.7344 (ttt180) REVERT: A 239 ARG cc_start: 0.8225 (mmt90) cc_final: 0.7934 (mmm-85) REVERT: B 131 ASN cc_start: 0.8344 (t0) cc_final: 0.8074 (t0) REVERT: B 213 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 239 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7111 (mmt180) REVERT: F 73 MET cc_start: 0.8359 (mmm) cc_final: 0.8158 (mtp) REVERT: F 147 LYS cc_start: 0.8055 (mttp) cc_final: 0.7572 (mttm) REVERT: F 212 ARG cc_start: 0.6908 (mtt90) cc_final: 0.6192 (mtp85) REVERT: F 326 ASP cc_start: 0.8947 (t0) cc_final: 0.8620 (t0) REVERT: G 208 MET cc_start: 0.7767 (tmm) cc_final: 0.7233 (tmm) outliers start: 13 outliers final: 11 residues processed: 139 average time/residue: 0.2535 time to fit residues: 47.0991 Evaluate side-chains 138 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9346 Z= 0.176 Angle : 0.507 7.751 12619 Z= 0.259 Chirality : 0.040 0.137 1433 Planarity : 0.004 0.042 1569 Dihedral : 12.615 156.147 1355 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.15 % Allowed : 12.51 % Favored : 86.34 % 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: 1.35 (0.26), residues: 1111 helix: 1.69 (0.21), residues: 604 sheet: 0.87 (0.43), residues: 143 loop : -0.38 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 257 HIS 0.002 0.000 HIS A 81 PHE 0.014 0.001 PHE G 194 TYR 0.008 0.001 TYR F 6 ARG 0.004 0.000 ARG F 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.033 Fit side-chains REVERT: A 33 GLU cc_start: 0.7608 (pt0) cc_final: 0.7331 (pt0) REVERT: A 239 ARG cc_start: 0.8204 (mmt90) cc_final: 0.7919 (mmm-85) REVERT: B 131 ASN cc_start: 0.8296 (t0) cc_final: 0.7973 (m-40) REVERT: B 226 GLU cc_start: 0.7748 (pt0) cc_final: 0.7462 (pt0) REVERT: B 239 ARG cc_start: 0.7647 (tpp80) cc_final: 0.7087 (mmt180) REVERT: F 147 LYS cc_start: 0.8052 (mttp) cc_final: 0.7557 (mttm) REVERT: F 212 ARG cc_start: 0.6888 (mtt90) cc_final: 0.6357 (mtt180) REVERT: F 213 ARG cc_start: 0.7175 (ttt-90) cc_final: 0.6625 (ttm-80) REVERT: F 326 ASP cc_start: 0.8927 (t0) cc_final: 0.8626 (t0) REVERT: G 208 MET cc_start: 0.7852 (tmm) cc_final: 0.7293 (tmm) outliers start: 11 outliers final: 10 residues processed: 136 average time/residue: 0.2340 time to fit residues: 43.4740 Evaluate side-chains 134 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0000 chunk 87 optimal weight: 0.7980 chunk 36 optimal weight: 0.0170 chunk 89 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 chunk 63 optimal weight: 10.0000 overall best weight: 0.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 HIS F 135 GLN ** F 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.145200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107363 restraints weight = 10787.332| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.03 r_work: 0.2880 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9346 Z= 0.129 Angle : 0.496 8.185 12619 Z= 0.251 Chirality : 0.039 0.173 1433 Planarity : 0.004 0.045 1569 Dihedral : 12.360 157.975 1355 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.83 % Allowed : 13.03 % Favored : 86.13 % 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: 1.51 (0.26), residues: 1111 helix: 1.86 (0.21), residues: 608 sheet: 0.78 (0.42), residues: 150 loop : -0.35 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 123 HIS 0.001 0.000 HIS A 81 PHE 0.013 0.001 PHE G 194 TYR 0.011 0.001 TYR G 162 ARG 0.004 0.000 ARG F 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.98 seconds wall clock time: 39 minutes 40.57 seconds (2380.57 seconds total)