Starting phenix.real_space_refine on Thu Mar 14 17:34:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufg_42206/03_2024/8ufg_42206_updated.pdb" } resolution = 3.1 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= 0.003 sd= 0.125 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 39 5.16 5 C 5897 2.51 5 N 1531 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 207": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9107 Number of models: 1 Model: "" Number of chains: 6 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: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain breaks: 2 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 173 Unusual residues: {'WJR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.29, per 1000 atoms: 0.58 Number of scatterers: 9107 At special positions: 0 Unit cell: (66, 109.725, 122.1, 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) S 39 16.00 P 2 15.00 O 1638 8.00 N 1531 7.00 C 5897 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 10 sheets defined 51.6% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 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: 3.901A pdb=" N ILE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.774A pdb=" N GLN A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) 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 148 through 162 removed outlier: 3.693A pdb=" N ALA A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 4.006A pdb=" N GLY A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 238 through 241 No H-bonds generated for 'chain 'A' and resid 238 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: 3.786A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.831A pdb=" N GLN B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) 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: 3.776A pdb=" N ALA B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 194 removed outlier: 4.200A pdb=" N GLY B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'F' and resid 3 through 39 Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 81 removed outlier: 3.750A 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 91 Processing helix chain 'F' and resid 95 through 118 Proline residue: F 104 - end of helix Processing helix chain 'F' and resid 120 through 135 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 263 through 274 Processing helix chain 'F' and resid 276 through 288 removed outlier: 4.063A pdb=" N VAL F 287 " --> pdb=" O MET F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 324 Processing helix chain 'F' and resid 330 through 348 Proline residue: F 334 - end of helix removed outlier: 3.580A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 38 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 94 Processing helix chain 'G' and resid 98 through 122 removed outlier: 4.047A pdb=" N VAL G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 135 removed outlier: 3.616A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 239 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 326 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: 6.433A pdb=" N ILE A 217 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 226 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 215 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS A 214 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 198 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU A 42 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.225A 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: 7.736A pdb=" N LYS A 19 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 5.447A 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: 6.285A pdb=" N ILE B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU B 226 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 215 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS B 214 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 198 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU B 42 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.273A 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: 7.771A pdb=" N LYS B 19 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 5.436A 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: 4.064A pdb=" N GLU F 148 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 159 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 192 through 194 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 168 through 170 removed outlier: 4.439A pdb=" N GLN G 191 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL G 195 " --> pdb=" O GLN G 199 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLN G 199 " --> pdb=" O VAL G 195 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1287 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: 2.72 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1440 1.31 - 1.44: 2434 1.44 - 1.56: 5332 1.56 - 1.68: 4 1.68 - 1.81: 72 Bond restraints: 9282 Sorted by residual: bond pdb=" C21 WJR G 401 " pdb=" N20 WJR G 401 " ideal model delta sigma weight residual 1.546 1.335 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C75 WJR G 401 " pdb=" N74 WJR G 401 " ideal model delta sigma weight residual 1.515 1.336 0.179 2.00e-02 2.50e+03 8.02e+01 bond pdb=" C19 WJR G 401 " pdb=" N20 WJR G 401 " ideal model delta sigma weight residual 1.596 1.454 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" CE8 WJR G 401 " pdb=" OE7 WJR G 401 " ideal model delta sigma weight residual 1.560 1.432 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" CE8 WJR G 401 " pdb=" CE9 WJR G 401 " ideal model delta sigma weight residual 1.404 1.532 -0.128 2.00e-02 2.50e+03 4.10e+01 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 71.22 - 83.77: 1 83.77 - 96.32: 0 96.32 - 108.86: 491 108.86 - 121.41: 9947 121.41 - 133.96: 2106 Bond angle restraints: 12545 Sorted by residual: angle pdb=" CE0 WJR G 401 " pdb=" CD9 WJR G 401 " pdb=" OK1 WJR G 401 " ideal model delta sigma weight residual 108.75 71.22 37.53 3.00e+00 1.11e-01 1.56e+02 angle pdb=" N ARG B 194 " pdb=" CA ARG B 194 " pdb=" C ARG B 194 " ideal model delta sigma weight residual 114.39 104.32 10.07 1.45e+00 4.76e-01 4.82e+01 angle pdb=" N LEU B 191 " pdb=" CA LEU B 191 " pdb=" C LEU B 191 " ideal model delta sigma weight residual 112.23 103.49 8.74 1.26e+00 6.30e-01 4.81e+01 angle pdb=" N ARG A 189 " pdb=" CA ARG A 189 " pdb=" C ARG A 189 " ideal model delta sigma weight residual 113.50 105.93 7.57 1.23e+00 6.61e-01 3.79e+01 angle pdb=" CE0 WJR G 401 " pdb=" CD9 WJR G 401 " pdb=" OD8 WJR G 401 " ideal model delta sigma weight residual 109.09 126.55 -17.46 3.00e+00 1.11e-01 3.39e+01 ... (remaining 12540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 5429 32.68 - 65.36: 145 65.36 - 98.04: 19 98.04 - 130.72: 4 130.72 - 163.40: 3 Dihedral angle restraints: 5600 sinusoidal: 2368 harmonic: 3232 Sorted by residual: dihedral pdb=" C79 WJR G 401 " pdb=" C80 WJR G 401 " pdb=" C81 WJR G 401 " pdb=" C82 WJR G 401 " ideal model delta sinusoidal sigma weight residual 138.91 -57.69 -163.40 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C93 WJR G 401 " pdb=" C94 WJR G 401 " pdb=" C95 WJR G 401 " pdb=" C96 WJR G 401 " ideal model delta sinusoidal sigma weight residual 154.10 -60.36 -145.54 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C1 WJR G 401 " pdb=" C2 WJR G 401 " pdb=" C3 WJR G 401 " pdb=" C4 WJR G 401 " ideal model delta sinusoidal sigma weight residual 192.63 47.75 144.88 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 5597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.010: 1445 1.010 - 2.020: 0 2.020 - 3.030: 0 3.030 - 4.040: 0 4.040 - 5.050: 1 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CB5 WJR G 401 " pdb=" CB6 WJR G 401 " pdb=" CB9 WJR G 401 " pdb=" OK7 WJR G 401 " both_signs ideal model delta sigma weight residual False 2.57 -2.48 5.05 2.00e-01 2.50e+01 6.38e+02 chirality pdb=" CJ6 WJR G 401 " pdb=" CI3 WJR G 401 " pdb=" CJ7 WJR G 401 " pdb=" OK1 WJR G 401 " both_signs ideal model delta sigma weight residual False -2.65 -2.39 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CK2 WJR G 401 " pdb=" CD7 WJR G 401 " pdb=" CK3 WJR G 401 " pdb=" OK7 WJR G 401 " both_signs ideal model delta sigma weight residual False -2.55 -2.30 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1443 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 36 " -0.025 2.00e-02 2.50e+03 4.86e-02 2.37e+01 pdb=" C SER B 36 " 0.084 2.00e-02 2.50e+03 pdb=" O SER B 36 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY B 37 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C73 WJR G 401 " -0.038 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" C75 WJR G 401 " 0.009 2.00e-02 2.50e+03 pdb=" C76 WJR G 401 " -0.029 2.00e-02 2.50e+03 pdb=" N74 WJR G 401 " 0.051 2.00e-02 2.50e+03 pdb=" OA3 WJR G 401 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 36 " 0.016 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C SER A 36 " -0.053 2.00e-02 2.50e+03 pdb=" O SER A 36 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY A 37 " 0.018 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 81 2.57 - 3.16: 7374 3.16 - 3.74: 14744 3.74 - 4.32: 20661 4.32 - 4.90: 34972 Nonbonded interactions: 77832 Sorted by model distance: nonbonded pdb=" OE1 WJR G 401 " pdb=" OK1 WJR G 401 " model vdw 1.993 2.432 nonbonded pdb=" OG1 THR G 23 " pdb=" OG SER G 70 " model vdw 2.221 2.440 nonbonded pdb=" O LEU F 118 " pdb=" OG SER F 253 " model vdw 2.259 2.440 nonbonded pdb=" O MET G 257 " pdb=" N SER G 261 " model vdw 2.279 2.520 nonbonded pdb=" OC4 WJR G 401 " pdb=" OJ8 WJR G 401 " model vdw 2.280 2.440 ... (remaining 77827 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: 0.790 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: 5.040 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.170 Find NCS groups from input model: 0.380 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.008 0.211 9282 Z= 0.527 Angle : 0.926 37.530 12545 Z= 0.441 Chirality : 0.142 5.050 1446 Planarity : 0.004 0.049 1552 Dihedral : 16.010 163.401 3522 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.11 % Allowed : 0.95 % Favored : 98.95 % 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: 1.04 (0.26), residues: 1100 helix: 1.52 (0.22), residues: 591 sheet: 0.87 (0.54), residues: 117 loop : -0.59 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 271 HIS 0.002 0.001 HIS B 203 PHE 0.036 0.001 PHE G 253 TYR 0.010 0.001 TYR F 6 ARG 0.006 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: B 204 ASN cc_start: 0.8464 (t0) cc_final: 0.8213 (t0) outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 0.2272 time to fit residues: 27.9949 Evaluate side-chains 76 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9282 Z= 0.352 Angle : 0.705 22.370 12545 Z= 0.315 Chirality : 0.071 2.102 1446 Planarity : 0.004 0.050 1552 Dihedral : 13.142 139.460 1402 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.74 % Allowed : 7.26 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1100 helix: 1.26 (0.22), residues: 592 sheet: 0.74 (0.48), residues: 130 loop : -0.49 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 331 HIS 0.004 0.001 HIS A 214 PHE 0.017 0.001 PHE G 253 TYR 0.009 0.001 TYR F 6 ARG 0.004 0.000 ARG F 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8374 (ttpt) REVERT: B 15 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7694 (mtpp) REVERT: B 94 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7547 (pm20) REVERT: B 204 ASN cc_start: 0.8532 (t0) cc_final: 0.8245 (t0) REVERT: F 255 LYS cc_start: 0.8313 (mttm) cc_final: 0.7914 (mtpt) REVERT: G 257 MET cc_start: 0.7480 (mtt) cc_final: 0.7078 (mtt) outliers start: 7 outliers final: 3 residues processed: 83 average time/residue: 0.2305 time to fit residues: 27.0404 Evaluate side-chains 80 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 190 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9282 Z= 0.197 Angle : 0.624 23.295 12545 Z= 0.275 Chirality : 0.067 2.029 1446 Planarity : 0.004 0.047 1552 Dihedral : 11.847 127.042 1402 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.63 % Allowed : 9.15 % Favored : 90.22 % 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: 1.00 (0.26), residues: 1100 helix: 1.35 (0.22), residues: 590 sheet: 0.79 (0.48), residues: 130 loop : -0.38 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 150 HIS 0.003 0.001 HIS A 214 PHE 0.010 0.001 PHE A 32 TYR 0.008 0.001 TYR F 6 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.022 Fit side-chains REVERT: A 186 ASP cc_start: 0.7368 (m-30) cc_final: 0.7027 (m-30) REVERT: A 191 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7824 (mp) REVERT: B 94 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7541 (pm20) REVERT: B 136 THR cc_start: 0.8390 (m) cc_final: 0.8138 (p) REVERT: B 204 ASN cc_start: 0.8522 (t0) cc_final: 0.8240 (t0) REVERT: F 255 LYS cc_start: 0.8286 (mttm) cc_final: 0.7892 (mtpt) REVERT: G 257 MET cc_start: 0.7565 (mtt) cc_final: 0.7293 (mtt) outliers start: 6 outliers final: 2 residues processed: 78 average time/residue: 0.2120 time to fit residues: 23.8497 Evaluate side-chains 77 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain F residue 47 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9282 Z= 0.414 Angle : 0.705 22.914 12545 Z= 0.318 Chirality : 0.070 2.010 1446 Planarity : 0.004 0.051 1552 Dihedral : 11.433 125.151 1398 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.47 % Allowed : 11.46 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1100 helix: 0.95 (0.21), residues: 591 sheet: 0.47 (0.46), residues: 137 loop : -0.45 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 331 HIS 0.004 0.001 HIS B 214 PHE 0.013 0.002 PHE F 277 TYR 0.011 0.001 TYR F 6 ARG 0.004 0.000 ARG F 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7299 (tpp-160) REVERT: A 191 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7837 (mp) REVERT: B 15 LYS cc_start: 0.8373 (ptpt) cc_final: 0.7809 (mtpp) REVERT: B 24 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7510 (ttp80) REVERT: B 204 ASN cc_start: 0.8536 (t0) cc_final: 0.8158 (t0) REVERT: B 207 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7234 (mm-30) REVERT: F 255 LYS cc_start: 0.8256 (mttm) cc_final: 0.7894 (mtmt) outliers start: 14 outliers final: 10 residues processed: 94 average time/residue: 0.2414 time to fit residues: 31.1968 Evaluate side-chains 95 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.0020 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS G 173 GLN ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9282 Z= 0.158 Angle : 0.611 24.081 12545 Z= 0.270 Chirality : 0.067 2.028 1446 Planarity : 0.004 0.047 1552 Dihedral : 10.866 120.264 1398 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.84 % Allowed : 13.14 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1100 helix: 1.29 (0.22), residues: 593 sheet: 0.63 (0.46), residues: 136 loop : -0.46 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 150 HIS 0.003 0.001 HIS B 214 PHE 0.016 0.001 PHE G 253 TYR 0.007 0.001 TYR F 6 ARG 0.004 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.992 Fit side-chains REVERT: A 186 ASP cc_start: 0.7459 (m-30) cc_final: 0.7081 (m-30) REVERT: B 15 LYS cc_start: 0.8273 (ptpt) cc_final: 0.7782 (mtpp) REVERT: B 136 THR cc_start: 0.8446 (m) cc_final: 0.8183 (p) REVERT: B 204 ASN cc_start: 0.8552 (t0) cc_final: 0.8253 (t0) REVERT: F 233 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6747 (tt) REVERT: F 255 LYS cc_start: 0.8282 (mttm) cc_final: 0.7943 (mtmt) REVERT: G 254 MET cc_start: 0.8119 (mtp) cc_final: 0.7917 (mtp) outliers start: 8 outliers final: 3 residues processed: 83 average time/residue: 0.2235 time to fit residues: 26.6088 Evaluate side-chains 80 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9282 Z= 0.330 Angle : 0.655 23.340 12545 Z= 0.293 Chirality : 0.068 2.014 1446 Planarity : 0.004 0.048 1552 Dihedral : 10.723 110.151 1398 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.10 % Allowed : 13.14 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1100 helix: 1.18 (0.21), residues: 590 sheet: 0.43 (0.45), residues: 136 loop : -0.46 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 272 HIS 0.003 0.001 HIS A 214 PHE 0.026 0.001 PHE G 253 TYR 0.010 0.001 TYR F 6 ARG 0.003 0.000 ARG F 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7546 (tpp-160) cc_final: 0.7305 (tpp-160) REVERT: B 15 LYS cc_start: 0.8309 (ptpt) cc_final: 0.7773 (mtpp) REVERT: B 204 ASN cc_start: 0.8528 (t0) cc_final: 0.8173 (t0) REVERT: B 207 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7277 (mm-30) REVERT: F 233 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6746 (tt) REVERT: F 255 LYS cc_start: 0.8283 (mttm) cc_final: 0.7942 (mtmt) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.2504 time to fit residues: 32.0772 Evaluate side-chains 93 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 206 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 10 GLN ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9282 Z= 0.371 Angle : 0.673 23.560 12545 Z= 0.303 Chirality : 0.069 2.017 1446 Planarity : 0.004 0.049 1552 Dihedral : 10.601 104.057 1398 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 13.35 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1100 helix: 0.99 (0.21), residues: 594 sheet: 0.25 (0.46), residues: 134 loop : -0.49 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 272 HIS 0.003 0.001 HIS A 214 PHE 0.026 0.001 PHE G 253 TYR 0.015 0.001 TYR F 299 ARG 0.004 0.000 ARG F 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7545 (tpp-160) cc_final: 0.7283 (tpp-160) REVERT: A 191 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 239 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7471 (mtm-85) REVERT: B 15 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7766 (mtpp) REVERT: B 24 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7327 (ttp80) REVERT: F 255 LYS cc_start: 0.8232 (mttm) cc_final: 0.7862 (mtpt) outliers start: 20 outliers final: 13 residues processed: 93 average time/residue: 0.2602 time to fit residues: 32.9063 Evaluate side-chains 94 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 284 MET Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain G residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9282 Z= 0.189 Angle : 0.617 24.144 12545 Z= 0.273 Chirality : 0.067 2.023 1446 Planarity : 0.004 0.048 1552 Dihedral : 10.146 99.272 1398 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.53 % Allowed : 15.35 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1100 helix: 1.26 (0.22), residues: 594 sheet: 0.24 (0.46), residues: 134 loop : -0.46 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 119 HIS 0.003 0.001 HIS B 214 PHE 0.024 0.001 PHE G 253 TYR 0.009 0.001 TYR G 256 ARG 0.002 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: B 15 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7766 (mtpp) REVERT: B 136 THR cc_start: 0.8431 (m) cc_final: 0.8178 (p) REVERT: B 204 ASN cc_start: 0.8592 (t0) cc_final: 0.8284 (t0) REVERT: B 207 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7240 (mm-30) REVERT: F 255 LYS cc_start: 0.8270 (mttm) cc_final: 0.7943 (mtmt) outliers start: 5 outliers final: 4 residues processed: 83 average time/residue: 0.2341 time to fit residues: 27.0884 Evaluate side-chains 85 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain F residue 47 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 0.0010 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 64 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9282 Z= 0.179 Angle : 0.610 23.990 12545 Z= 0.269 Chirality : 0.067 2.023 1446 Planarity : 0.004 0.048 1552 Dihedral : 9.823 90.148 1398 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.95 % Allowed : 14.83 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1100 helix: 1.38 (0.22), residues: 593 sheet: 0.26 (0.46), residues: 134 loop : -0.45 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 150 HIS 0.003 0.001 HIS B 214 PHE 0.025 0.001 PHE G 253 TYR 0.007 0.001 TYR F 6 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.886 Fit side-chains REVERT: A 186 ASP cc_start: 0.7481 (m-30) cc_final: 0.7107 (m-30) REVERT: A 191 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7820 (mp) REVERT: B 15 LYS cc_start: 0.8331 (ptpt) cc_final: 0.7866 (mtpp) REVERT: B 132 ASP cc_start: 0.8082 (t0) cc_final: 0.7727 (m-30) REVERT: B 136 THR cc_start: 0.8432 (m) cc_final: 0.8184 (p) REVERT: B 204 ASN cc_start: 0.8596 (t0) cc_final: 0.8310 (t0) REVERT: B 207 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7220 (mm-30) REVERT: F 120 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7344 (mtp) REVERT: F 255 LYS cc_start: 0.8262 (mttm) cc_final: 0.7961 (mtmt) outliers start: 9 outliers final: 5 residues processed: 87 average time/residue: 0.2288 time to fit residues: 28.1196 Evaluate side-chains 87 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9282 Z= 0.222 Angle : 0.621 23.935 12545 Z= 0.275 Chirality : 0.067 2.021 1446 Planarity : 0.004 0.048 1552 Dihedral : 9.713 87.923 1398 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.84 % Allowed : 14.83 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1100 helix: 1.33 (0.21), residues: 593 sheet: 0.24 (0.46), residues: 134 loop : -0.45 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 272 HIS 0.003 0.001 HIS B 214 PHE 0.027 0.001 PHE G 253 TYR 0.012 0.001 TYR F 299 ARG 0.002 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.012 Fit side-chains REVERT: A 186 ASP cc_start: 0.7452 (m-30) cc_final: 0.7063 (m-30) REVERT: A 191 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7854 (mp) REVERT: B 15 LYS cc_start: 0.8335 (ptpt) cc_final: 0.7881 (mtpp) REVERT: B 204 ASN cc_start: 0.8606 (t0) cc_final: 0.8317 (t0) REVERT: B 207 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7219 (mm-30) REVERT: F 120 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7331 (mtp) REVERT: F 255 LYS cc_start: 0.8319 (mttm) cc_final: 0.8029 (mtmt) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 0.2290 time to fit residues: 27.3033 Evaluate side-chains 86 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 120 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** 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 = 0.3473 r_free = 0.3473 target = 0.138133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.100109 restraints weight = 9614.240| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.58 r_work: 0.2884 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9282 Z= 0.212 Angle : 0.618 24.063 12545 Z= 0.274 Chirality : 0.067 2.022 1446 Planarity : 0.004 0.047 1552 Dihedral : 9.582 88.823 1398 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.05 % Allowed : 14.72 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1100 helix: 1.35 (0.21), residues: 592 sheet: 0.24 (0.46), residues: 134 loop : -0.43 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 150 HIS 0.003 0.001 HIS B 214 PHE 0.025 0.001 PHE G 253 TYR 0.008 0.001 TYR F 6 ARG 0.002 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1871.51 seconds wall clock time: 34 minutes 28.22 seconds (2068.22 seconds total)