Starting phenix.real_space_refine on Tue Feb 13 15:22:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/02_2024/7qud_14148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/02_2024/7qud_14148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/02_2024/7qud_14148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/02_2024/7qud_14148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/02_2024/7qud_14148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/02_2024/7qud_14148_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 6 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 4214 2.51 5 N 1137 2.21 5 O 1291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6696 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3350 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3281 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 397} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.97, per 1000 atoms: 0.59 Number of scatterers: 6696 At special positions: 0 Unit cell: (97.032, 74.64, 101.386, 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) S 47 16.00 P 6 15.00 Mg 1 11.99 O 1291 8.00 N 1137 7.00 C 4214 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: 2.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 5 sheets defined 47.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.951A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 110 through 128 removed outlier: 3.976A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.475A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.976A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.869A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.910A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.225A pdb=" N ARG A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.973A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 3.654A pdb=" N VAL A 435 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 71 through 78 removed outlier: 3.683A pdb=" N SER B 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 124 removed outlier: 4.876A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 158 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.655A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.678A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 372 through 391 removed outlier: 4.335A pdb=" N PHE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG B 390 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.538A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 427 Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 8.637A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 9 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ILE A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 167 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.492A pdb=" N LYS A 352 " --> pdb=" O MET A 317 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TYR A 319 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY A 354 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N GLY A 321 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.134A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS B 6 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 9 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N HIS B 137 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 170 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 202 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 267 through 271 276 hydrogen bonds defined for protein. 672 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: 1.83 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2212 1.34 - 1.46: 1547 1.46 - 1.58: 3004 1.58 - 1.70: 10 1.70 - 1.82: 74 Bond restraints: 6847 Sorted by residual: bond pdb=" CG1 ILE A 122 " pdb=" CD1 ILE A 122 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.16e+00 bond pdb=" CG1 ILE A 234 " pdb=" CD1 ILE A 234 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 bond pdb=" CA THR B 219 " pdb=" C THR B 219 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.16e-01 bond pdb=" CB GLN A 35 " pdb=" CG GLN A 35 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.53e-01 bond pdb=" CG GLN B 245 " pdb=" CD GLN B 245 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.31e-01 ... (remaining 6842 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.17: 196 106.17 - 113.13: 3642 113.13 - 120.10: 2502 120.10 - 127.06: 2884 127.06 - 134.02: 78 Bond angle restraints: 9302 Sorted by residual: angle pdb=" C THR B 218 " pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta sigma weight residual 122.83 126.19 -3.36 1.08e+00 8.57e-01 9.67e+00 angle pdb=" C PRO B 261 " pdb=" N ARG B 262 " pdb=" CA ARG B 262 " ideal model delta sigma weight residual 124.82 129.55 -4.73 1.78e+00 3.16e-01 7.07e+00 angle pdb=" CA MET A 317 " pdb=" CB MET A 317 " pdb=" CG MET A 317 " ideal model delta sigma weight residual 114.10 119.02 -4.92 2.00e+00 2.50e-01 6.06e+00 angle pdb=" CB MET B 300 " pdb=" CG MET B 300 " pdb=" SD MET B 300 " ideal model delta sigma weight residual 112.70 119.59 -6.89 3.00e+00 1.11e-01 5.27e+00 angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 104.56 6.44 3.00e+00 1.11e-01 4.60e+00 ... (remaining 9297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 3956 33.24 - 66.49: 85 66.49 - 99.73: 21 99.73 - 132.97: 2 132.97 - 166.22: 3 Dihedral angle restraints: 4067 sinusoidal: 1630 harmonic: 2437 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -61.62 166.22 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -128.12 -162.61 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -82.06 151.33 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 4064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 792 0.050 - 0.100: 190 0.100 - 0.150: 38 0.150 - 0.200: 0 0.200 - 0.250: 1 Chirality restraints: 1021 Sorted by residual: chirality pdb=" CG LEU A 425 " pdb=" CB LEU A 425 " pdb=" CD1 LEU A 425 " pdb=" CD2 LEU A 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU B 181 " pdb=" N GLU B 181 " pdb=" C GLU B 181 " pdb=" CB GLU B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA LEU A 425 " pdb=" N LEU A 425 " pdb=" C LEU A 425 " pdb=" CB LEU A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1018 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 260 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO B 261 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 267 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 268 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 271 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 272 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.025 5.00e-02 4.00e+02 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 97 2.61 - 3.18: 5995 3.18 - 3.75: 10591 3.75 - 4.33: 14985 4.33 - 4.90: 24740 Nonbonded interactions: 56408 Sorted by model distance: nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.033 2.170 nonbonded pdb=" O GLY B 141 " pdb=" OG SER B 145 " model vdw 2.143 2.440 nonbonded pdb=" OD1 ASN A 186 " pdb=" OH TYR A 408 " model vdw 2.184 2.440 nonbonded pdb=" O GLY A 416 " pdb=" OG SER A 419 " model vdw 2.184 2.440 nonbonded pdb=" OH TYR A 210 " pdb=" NH1 ARG A 221 " model vdw 2.185 2.520 ... (remaining 56403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 5.860 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.870 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6847 Z= 0.273 Angle : 0.616 6.887 9302 Z= 0.324 Chirality : 0.044 0.250 1021 Planarity : 0.005 0.067 1206 Dihedral : 16.741 166.216 2503 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.13 (0.29), residues: 834 helix: 0.70 (0.27), residues: 362 sheet: -0.69 (0.45), residues: 127 loop : -0.56 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 21 HIS 0.006 0.001 HIS A 266 PHE 0.011 0.002 PHE A 138 TYR 0.017 0.002 TYR B 36 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3969 (tmm) cc_final: 0.3313 (tmm) REVERT: A 27 GLU cc_start: 0.6970 (tp30) cc_final: 0.6656 (tp30) REVERT: A 155 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6578 (mt-10) REVERT: A 311 LYS cc_start: 0.7075 (mtpp) cc_final: 0.6317 (mmtp) REVERT: B 23 ILE cc_start: 0.8787 (mm) cc_final: 0.8586 (mm) REVERT: B 30 ILE cc_start: 0.6442 (mt) cc_final: 0.6235 (mt) REVERT: B 69 GLU cc_start: 0.6817 (pt0) cc_final: 0.6412 (pm20) REVERT: B 108 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6351 (tt0) REVERT: B 202 ILE cc_start: 0.8107 (mm) cc_final: 0.7907 (mt) REVERT: B 207 LEU cc_start: 0.8440 (mm) cc_final: 0.8202 (mm) REVERT: B 256 ASN cc_start: 0.7642 (t160) cc_final: 0.7439 (t0) REVERT: B 257 MET cc_start: 0.8263 (mmm) cc_final: 0.7295 (mmt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1849 time to fit residues: 43.7078 Evaluate side-chains 130 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.0020 chunk 48 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6847 Z= 0.257 Angle : 0.582 6.907 9302 Z= 0.299 Chirality : 0.044 0.190 1021 Planarity : 0.006 0.069 1206 Dihedral : 12.623 166.915 942 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.95 % Allowed : 9.61 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.16 (0.29), residues: 834 helix: 0.63 (0.27), residues: 363 sheet: -0.58 (0.45), residues: 131 loop : -0.59 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 346 HIS 0.005 0.001 HIS A 266 PHE 0.019 0.002 PHE A 49 TYR 0.014 0.001 TYR A 262 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3871 (tmm) cc_final: 0.3217 (tmm) REVERT: A 155 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6559 (mt-10) REVERT: A 311 LYS cc_start: 0.6976 (mtpp) cc_final: 0.6382 (mmtm) REVERT: B 30 ILE cc_start: 0.6382 (mt) cc_final: 0.6167 (mt) REVERT: B 69 GLU cc_start: 0.6852 (pt0) cc_final: 0.6286 (pm20) REVERT: B 108 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6332 (tt0) REVERT: B 154 LYS cc_start: 0.8346 (mmtt) cc_final: 0.8011 (mmtm) REVERT: B 207 LEU cc_start: 0.8499 (mm) cc_final: 0.8260 (mm) REVERT: B 256 ASN cc_start: 0.7632 (t0) cc_final: 0.7427 (t0) REVERT: B 257 MET cc_start: 0.8180 (mmm) cc_final: 0.7202 (mmt) REVERT: B 412 GLU cc_start: 0.7999 (pt0) cc_final: 0.7683 (pt0) outliers start: 14 outliers final: 11 residues processed: 146 average time/residue: 0.1652 time to fit residues: 33.1724 Evaluate side-chains 140 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 6847 Z= 0.160 Angle : 0.524 7.236 9302 Z= 0.266 Chirality : 0.042 0.155 1021 Planarity : 0.005 0.060 1206 Dihedral : 12.377 170.713 942 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.81 % Allowed : 12.40 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.02 (0.29), residues: 834 helix: 0.79 (0.27), residues: 362 sheet: -0.48 (0.45), residues: 136 loop : -0.56 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 101 HIS 0.003 0.001 HIS B 6 PHE 0.015 0.001 PHE A 49 TYR 0.012 0.001 TYR A 210 ARG 0.002 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3639 (tmm) cc_final: 0.2860 (tmm) REVERT: A 155 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6511 (mt-10) REVERT: A 311 LYS cc_start: 0.6893 (mtpp) cc_final: 0.6295 (mmtm) REVERT: A 388 TRP cc_start: 0.8016 (m100) cc_final: 0.7745 (m100) REVERT: B 30 ILE cc_start: 0.6322 (mt) cc_final: 0.6115 (mt) REVERT: B 108 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6299 (tt0) REVERT: B 154 LYS cc_start: 0.8322 (mmtt) cc_final: 0.7993 (mmtm) REVERT: B 207 LEU cc_start: 0.8496 (mm) cc_final: 0.8214 (mm) REVERT: B 257 MET cc_start: 0.8106 (mmm) cc_final: 0.7122 (mmt) REVERT: B 412 GLU cc_start: 0.8028 (pt0) cc_final: 0.7664 (pt0) outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 0.1742 time to fit residues: 36.2292 Evaluate side-chains 139 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6847 Z= 0.242 Angle : 0.562 8.139 9302 Z= 0.290 Chirality : 0.043 0.141 1021 Planarity : 0.005 0.066 1206 Dihedral : 12.591 175.340 942 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.06 % Allowed : 14.07 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.11 (0.29), residues: 834 helix: 0.65 (0.27), residues: 363 sheet: -0.46 (0.45), residues: 136 loop : -0.57 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 101 HIS 0.005 0.001 HIS A 266 PHE 0.021 0.002 PHE B 367 TYR 0.012 0.001 TYR A 210 ARG 0.004 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3651 (tmm) cc_final: 0.2794 (tmm) REVERT: A 155 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6549 (mt-10) REVERT: A 234 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 262 TYR cc_start: 0.7082 (m-80) cc_final: 0.6788 (m-80) REVERT: A 311 LYS cc_start: 0.6829 (mtpp) cc_final: 0.6265 (mmtm) REVERT: A 373 ARG cc_start: 0.7527 (ptp90) cc_final: 0.7301 (ptp90) REVERT: A 388 TRP cc_start: 0.8070 (m100) cc_final: 0.7800 (m100) REVERT: B 108 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6386 (tt0) REVERT: B 154 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8019 (mmtm) REVERT: B 207 LEU cc_start: 0.8547 (mm) cc_final: 0.8231 (mm) REVERT: B 257 MET cc_start: 0.8150 (mmm) cc_final: 0.7123 (mmt) REVERT: B 412 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7626 (pt0) outliers start: 22 outliers final: 15 residues processed: 148 average time/residue: 0.1644 time to fit residues: 33.6162 Evaluate side-chains 139 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6847 Z= 0.337 Angle : 0.619 8.414 9302 Z= 0.321 Chirality : 0.045 0.184 1021 Planarity : 0.006 0.071 1206 Dihedral : 12.883 174.363 942 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.48 % Allowed : 16.16 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.35 (0.29), residues: 834 helix: 0.43 (0.27), residues: 363 sheet: -0.55 (0.47), residues: 132 loop : -0.70 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 101 HIS 0.007 0.001 HIS A 266 PHE 0.014 0.002 PHE B 133 TYR 0.013 0.002 TYR B 51 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3716 (tmm) cc_final: 0.3051 (tmm) REVERT: A 155 GLU cc_start: 0.6862 (mt-10) cc_final: 0.6582 (mt-10) REVERT: A 234 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8631 (mp) REVERT: A 255 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: A 262 TYR cc_start: 0.7082 (m-80) cc_final: 0.6824 (m-80) REVERT: A 311 LYS cc_start: 0.6843 (mtpp) cc_final: 0.6281 (mmtm) REVERT: A 373 ARG cc_start: 0.7553 (ptp90) cc_final: 0.7292 (ptp90) REVERT: B 108 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6398 (mm-30) REVERT: B 154 LYS cc_start: 0.8375 (mmtt) cc_final: 0.8038 (mmtm) REVERT: B 207 LEU cc_start: 0.8575 (mm) cc_final: 0.8258 (mm) REVERT: B 412 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7634 (pt0) outliers start: 25 outliers final: 19 residues processed: 145 average time/residue: 0.1620 time to fit residues: 32.0586 Evaluate side-chains 145 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 47 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6847 Z= 0.154 Angle : 0.523 7.023 9302 Z= 0.269 Chirality : 0.041 0.158 1021 Planarity : 0.005 0.063 1206 Dihedral : 12.342 164.782 942 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.65 % Allowed : 17.83 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.06 (0.29), residues: 834 helix: 0.72 (0.27), residues: 361 sheet: -0.40 (0.46), residues: 136 loop : -0.60 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 101 HIS 0.003 0.001 HIS B 6 PHE 0.024 0.001 PHE B 367 TYR 0.012 0.001 TYR A 210 ARG 0.002 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3424 (tmm) cc_final: 0.2799 (tmm) REVERT: A 155 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6496 (mt-10) REVERT: A 234 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8600 (mp) REVERT: A 255 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: A 262 TYR cc_start: 0.6860 (m-80) cc_final: 0.6617 (m-80) REVERT: A 311 LYS cc_start: 0.6795 (mtpp) cc_final: 0.6531 (tppt) REVERT: B 108 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6334 (tt0) REVERT: B 154 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7996 (mmtm) REVERT: B 207 LEU cc_start: 0.8572 (mm) cc_final: 0.8266 (mm) REVERT: B 412 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7587 (pt0) outliers start: 19 outliers final: 11 residues processed: 148 average time/residue: 0.1671 time to fit residues: 33.9324 Evaluate side-chains 141 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 0.034 6847 Z= 0.207 Angle : 0.551 7.455 9302 Z= 0.283 Chirality : 0.042 0.147 1021 Planarity : 0.005 0.067 1206 Dihedral : 12.283 164.719 942 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.34 % Allowed : 17.13 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.10 (0.29), residues: 834 helix: 0.67 (0.27), residues: 362 sheet: -0.36 (0.47), residues: 135 loop : -0.62 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 101 HIS 0.004 0.001 HIS A 266 PHE 0.009 0.001 PHE B 20 TYR 0.012 0.001 TYR A 210 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3387 (tmm) cc_final: 0.2731 (tmm) REVERT: A 155 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6518 (mt-10) REVERT: A 234 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8606 (mp) REVERT: A 255 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7287 (m-10) REVERT: A 262 TYR cc_start: 0.6819 (m-80) cc_final: 0.6583 (m-80) REVERT: A 311 LYS cc_start: 0.6809 (mtpp) cc_final: 0.6288 (mmtm) REVERT: B 108 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6332 (tt0) REVERT: B 154 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7998 (mmtm) REVERT: B 207 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8235 (mm) REVERT: B 412 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7551 (pt0) outliers start: 24 outliers final: 15 residues processed: 145 average time/residue: 0.1616 time to fit residues: 32.3312 Evaluate side-chains 147 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 76 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6847 Z= 0.189 Angle : 0.543 7.889 9302 Z= 0.278 Chirality : 0.042 0.145 1021 Planarity : 0.005 0.066 1206 Dihedral : 12.122 164.323 942 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.79 % Allowed : 17.83 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.08 (0.29), residues: 834 helix: 0.69 (0.27), residues: 361 sheet: -0.36 (0.47), residues: 134 loop : -0.61 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.003 0.001 HIS A 266 PHE 0.025 0.001 PHE B 367 TYR 0.012 0.001 TYR A 210 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3238 (tmm) cc_final: 0.2636 (tmm) REVERT: A 155 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6528 (mt-10) REVERT: A 234 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8599 (mp) REVERT: A 255 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7218 (m-10) REVERT: A 262 TYR cc_start: 0.6723 (m-80) cc_final: 0.6511 (m-80) REVERT: A 311 LYS cc_start: 0.6813 (mtpp) cc_final: 0.6455 (mptt) REVERT: B 108 GLU cc_start: 0.6606 (mm-30) cc_final: 0.6290 (tt0) REVERT: B 154 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7999 (mmtm) REVERT: B 207 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 257 MET cc_start: 0.8153 (mmm) cc_final: 0.7077 (mmt) REVERT: B 398 TYR cc_start: 0.7965 (m-80) cc_final: 0.7582 (m-80) REVERT: B 412 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7553 (pt0) outliers start: 20 outliers final: 14 residues processed: 149 average time/residue: 0.1429 time to fit residues: 29.5079 Evaluate side-chains 150 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6847 Z= 0.178 Angle : 0.543 8.425 9302 Z= 0.277 Chirality : 0.042 0.153 1021 Planarity : 0.005 0.068 1206 Dihedral : 11.977 163.983 942 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.79 % Allowed : 17.83 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.06 (0.29), residues: 834 helix: 0.73 (0.27), residues: 361 sheet: -0.35 (0.46), residues: 135 loop : -0.63 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.003 0.001 HIS A 266 PHE 0.008 0.001 PHE B 20 TYR 0.011 0.001 TYR A 210 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3219 (tmm) cc_final: 0.2642 (tmm) REVERT: A 155 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6540 (mt-10) REVERT: A 234 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 255 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: A 311 LYS cc_start: 0.6774 (mtpp) cc_final: 0.6439 (mptt) REVERT: B 69 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6162 (mp0) REVERT: B 108 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6331 (tt0) REVERT: B 154 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7995 (mmtm) REVERT: B 207 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 257 MET cc_start: 0.8156 (mmm) cc_final: 0.7402 (mmt) REVERT: B 398 TYR cc_start: 0.7956 (m-80) cc_final: 0.7578 (m-80) REVERT: B 412 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7563 (pt0) outliers start: 20 outliers final: 15 residues processed: 151 average time/residue: 0.1780 time to fit residues: 36.1614 Evaluate side-chains 155 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6847 Z= 0.186 Angle : 0.557 8.621 9302 Z= 0.284 Chirality : 0.042 0.172 1021 Planarity : 0.005 0.070 1206 Dihedral : 11.928 164.024 942 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.79 % Allowed : 18.52 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.05 (0.29), residues: 834 helix: 0.72 (0.27), residues: 361 sheet: -0.31 (0.47), residues: 135 loop : -0.63 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.003 0.001 HIS A 197 PHE 0.028 0.001 PHE B 367 TYR 0.016 0.001 TYR A 210 ARG 0.005 0.000 ARG B 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3182 (tmm) cc_final: 0.2626 (tmm) REVERT: A 155 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6674 (mt-10) REVERT: A 234 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 255 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7252 (m-10) REVERT: A 311 LYS cc_start: 0.6767 (mtpp) cc_final: 0.6426 (mptt) REVERT: A 357 TYR cc_start: 0.6720 (m-80) cc_final: 0.6411 (m-80) REVERT: B 69 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: B 101 TRP cc_start: 0.6894 (t60) cc_final: 0.6650 (t60) REVERT: B 108 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6322 (tt0) REVERT: B 154 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8018 (mmtm) REVERT: B 207 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8229 (mm) REVERT: B 257 MET cc_start: 0.8146 (mmm) cc_final: 0.7412 (mmt) REVERT: B 398 TYR cc_start: 0.7960 (m-80) cc_final: 0.7595 (m-80) REVERT: B 412 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7566 (pt0) outliers start: 20 outliers final: 14 residues processed: 151 average time/residue: 0.1866 time to fit residues: 38.2260 Evaluate side-chains 153 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 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 = 0.4188 r_free = 0.4188 target = 0.166642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.142487 restraints weight = 10386.026| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.64 r_work: 0.3780 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6847 Z= 0.180 Angle : 0.557 8.313 9302 Z= 0.284 Chirality : 0.042 0.151 1021 Planarity : 0.005 0.067 1206 Dihedral : 11.863 163.958 942 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.79 % Allowed : 18.80 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.01 (0.29), residues: 834 helix: 0.75 (0.27), residues: 360 sheet: -0.28 (0.47), residues: 135 loop : -0.59 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.002 0.001 HIS A 266 PHE 0.008 0.001 PHE B 20 TYR 0.017 0.001 TYR A 210 ARG 0.005 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.24 seconds wall clock time: 34 minutes 38.23 seconds (2078.23 seconds total)