Starting phenix.real_space_refine on Wed Feb 14 04:25:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/02_2024/7zla_14778_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/02_2024/7zla_14778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/02_2024/7zla_14778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/02_2024/7zla_14778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/02_2024/7zla_14778_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/02_2024/7zla_14778_updated.pdb" } resolution = 3.99 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= 1.000 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 94 5.49 5 S 18 5.16 5 C 5227 2.51 5 N 1497 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "B TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 357": "OD1" <-> "OD2" 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: 8624 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2995 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 347} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3743 Classifications: {'peptide': 458} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 935 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 951 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Time building chain proxies: 5.25, per 1000 atoms: 0.61 Number of scatterers: 8624 At special positions: 0 Unit cell: (83.566, 112.014, 131.572, 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 18 16.00 P 94 15.00 O 1788 8.00 N 1497 7.00 C 5227 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: 4.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 5 sheets defined 38.2% alpha, 8.4% beta 32 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 121 through 131 removed outlier: 4.028A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 149 through 163 removed outlier: 3.818A pdb=" N ILE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 179 through 189 removed outlier: 4.408A pdb=" N GLN A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.895A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.978A pdb=" N GLN A 347 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL A 348 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 383 removed outlier: 4.008A pdb=" N ARG A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.880A pdb=" N ALA A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 448 through 462 removed outlier: 5.310A pdb=" N GLU A 452 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 455 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 29 removed outlier: 4.026A pdb=" N ALA B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 25 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 48 Processing helix chain 'B' and resid 53 through 61 removed outlier: 4.200A pdb=" N ALA B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 121 through 130 removed outlier: 3.760A pdb=" N GLN B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 149 through 162 removed outlier: 3.642A pdb=" N HIS B 161 " --> pdb=" O TYR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 179 through 189 removed outlier: 4.080A pdb=" N GLN B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.680A pdb=" N LEU B 209 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 205 through 210' Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 324 through 333 Processing helix chain 'B' and resid 343 through 354 removed outlier: 4.145A pdb=" N ALA B 351 " --> pdb=" O GLN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 381 Processing helix chain 'B' and resid 408 through 417 removed outlier: 3.703A pdb=" N LEU B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 removed outlier: 4.467A pdb=" N GLU B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.559A pdb=" N ILE A 273 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU A 304 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU A 275 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA A 306 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 238 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASP A 215 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE A 197 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL A 217 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 387 through 390 removed outlier: 4.074A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 402 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.558A pdb=" N GLY B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 303 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 273 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU B 304 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU B 275 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ALA B 306 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 194 through 196 removed outlier: 6.664A pdb=" N ASP B 215 " --> pdb=" O TYR B 195 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 387 through 390 removed outlier: 3.583A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 390 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 399 " --> pdb=" O ILE B 390 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1965 1.33 - 1.45: 2321 1.45 - 1.57: 4516 1.57 - 1.69: 184 1.69 - 1.81: 32 Bond restraints: 9018 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.730 1.547 0.183 2.00e-02 2.50e+03 8.35e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.730 1.548 0.182 2.00e-02 2.50e+03 8.24e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.313 1.437 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.313 1.434 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" OP2 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.586 1.475 0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 9013 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.14: 485 105.14 - 112.37: 4679 112.37 - 119.60: 3139 119.60 - 126.82: 3969 126.82 - 134.05: 341 Bond angle restraints: 12613 Sorted by residual: angle pdb=" N LYS A 367 " pdb=" CA LYS A 367 " pdb=" C LYS A 367 " ideal model delta sigma weight residual 111.14 104.92 6.22 1.08e+00 8.57e-01 3.32e+01 angle pdb=" C TYR A 278 " pdb=" CA TYR A 278 " pdb=" CB TYR A 278 " ideal model delta sigma weight residual 117.23 111.22 6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.00 109.59 10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N LYS A 367 " pdb=" CA LYS A 367 " pdb=" CB LYS A 367 " ideal model delta sigma weight residual 110.07 105.23 4.84 1.45e+00 4.76e-01 1.11e+01 angle pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " pdb=" C4 LLP A 309 " ideal model delta sigma weight residual 120.00 110.13 9.87 3.00e+00 1.11e-01 1.08e+01 ... (remaining 12608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 4583 29.58 - 59.16: 556 59.16 - 88.73: 37 88.73 - 118.31: 1 118.31 - 147.89: 3 Dihedral angle restraints: 5180 sinusoidal: 2752 harmonic: 2428 Sorted by residual: dihedral pdb=" CA HIS B 137 " pdb=" C HIS B 137 " pdb=" N ARG B 138 " pdb=" CA ARG B 138 " ideal model delta harmonic sigma weight residual -180.00 -153.80 -26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA HIS B 298 " pdb=" C HIS B 298 " pdb=" N ASN B 299 " pdb=" CA ASN B 299 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ASP A 199 " pdb=" C ASP A 199 " pdb=" N PRO A 200 " pdb=" CA PRO A 200 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 5177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 962 0.045 - 0.090: 316 0.090 - 0.136: 92 0.136 - 0.181: 10 0.181 - 0.226: 3 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CB ILE A 231 " pdb=" CA ILE A 231 " pdb=" CG1 ILE A 231 " pdb=" CG2 ILE A 231 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA LYS A 367 " pdb=" N LYS A 367 " pdb=" C LYS A 367 " pdb=" CB LYS A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG B 382 " pdb=" N ARG B 382 " pdb=" C ARG B 382 " pdb=" CB ARG B 382 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1380 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.166 2.00e-02 2.50e+03 2.96e-01 8.75e+02 pdb=" NZ LLP A 309 " -0.409 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.128 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.372 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 378 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C SER B 378 " 0.050 2.00e-02 2.50e+03 pdb=" O SER B 378 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 379 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 370 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ARG B 370 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG B 370 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 371 " -0.015 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 897 2.74 - 3.28: 8505 3.28 - 3.82: 14550 3.82 - 4.36: 16777 4.36 - 4.90: 26042 Nonbonded interactions: 66771 Sorted by model distance: nonbonded pdb=" O MET A 132 " pdb=" NH2 ARG B 125 " model vdw 2.198 2.520 nonbonded pdb=" OE1 GLU B 148 " pdb=" NE2 GLN B 347 " model vdw 2.203 2.520 nonbonded pdb=" OH TYR B 127 " pdb=" OE1 GLN B 355 " model vdw 2.205 2.440 nonbonded pdb=" O LYS A 386 " pdb=" NZ LYS A 403 " model vdw 2.213 2.520 nonbonded pdb=" OD2 ASP A 115 " pdb=" NZ LYS A 372 " model vdw 2.216 2.520 ... (remaining 66766 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 group one per residue 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.040 Find NCS groups from input model: 0.180 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 0.183 9018 Z= 0.508 Angle : 0.829 10.409 12613 Z= 0.476 Chirality : 0.048 0.226 1383 Planarity : 0.010 0.296 1288 Dihedral : 21.774 147.890 3624 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.94 (0.28), residues: 812 helix: -1.06 (0.29), residues: 306 sheet: -0.84 (0.50), residues: 85 loop : -1.51 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 264 HIS 0.008 0.002 HIS B 338 PHE 0.020 0.003 PHE B 247 TYR 0.025 0.002 TYR A 212 ARG 0.006 0.001 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.6770 (mmm) cc_final: 0.6561 (mmt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1990 time to fit residues: 25.3548 Evaluate side-chains 57 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS B 145 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9018 Z= 0.332 Angle : 0.750 9.748 12613 Z= 0.407 Chirality : 0.047 0.157 1383 Planarity : 0.006 0.051 1288 Dihedral : 24.989 148.054 1975 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.51 % Allowed : 9.48 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.89 (0.28), residues: 812 helix: -1.05 (0.29), residues: 308 sheet: -0.46 (0.54), residues: 85 loop : -1.55 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 264 HIS 0.007 0.002 HIS A 137 PHE 0.022 0.003 PHE A 352 TYR 0.018 0.002 TYR B 202 ARG 0.005 0.001 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 123 GLN cc_start: 0.6821 (tp-100) cc_final: 0.6332 (pt0) REVERT: A 202 TYR cc_start: 0.6739 (t80) cc_final: 0.6535 (t80) REVERT: B 110 HIS cc_start: 0.8524 (t-90) cc_final: 0.7786 (t70) REVERT: B 320 MET cc_start: 0.6017 (tmm) cc_final: 0.5817 (tmm) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.1901 time to fit residues: 20.9026 Evaluate side-chains 66 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 234 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9018 Z= 0.301 Angle : 0.712 9.185 12613 Z= 0.386 Chirality : 0.046 0.165 1383 Planarity : 0.005 0.051 1288 Dihedral : 25.080 147.549 1975 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.61 % Allowed : 14.70 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.79 (0.28), residues: 812 helix: -0.92 (0.29), residues: 308 sheet: -0.14 (0.56), residues: 85 loop : -1.61 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 264 HIS 0.006 0.001 HIS A 137 PHE 0.020 0.003 PHE B 352 TYR 0.018 0.002 TYR B 17 ARG 0.004 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: B 110 HIS cc_start: 0.8511 (t-90) cc_final: 0.7823 (t70) REVERT: B 406 MET cc_start: 0.4610 (tmm) cc_final: 0.4374 (tmm) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.1847 time to fit residues: 21.1286 Evaluate side-chains 69 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9018 Z= 0.334 Angle : 0.743 9.293 12613 Z= 0.403 Chirality : 0.047 0.169 1383 Planarity : 0.006 0.051 1288 Dihedral : 25.220 147.230 1975 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.71 % Allowed : 15.80 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.84 (0.28), residues: 812 helix: -0.86 (0.29), residues: 300 sheet: -0.04 (0.57), residues: 85 loop : -1.75 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 264 HIS 0.007 0.002 HIS A 137 PHE 0.020 0.003 PHE B 352 TYR 0.023 0.002 TYR B 17 ARG 0.003 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 61 time to evaluate : 0.867 Fit side-chains REVERT: A 403 LYS cc_start: 0.7772 (pttt) cc_final: 0.7369 (tppt) REVERT: A 407 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7153 (p0) REVERT: B 110 HIS cc_start: 0.8542 (t-90) cc_final: 0.8003 (t70) REVERT: B 202 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.5209 (t80) REVERT: B 406 MET cc_start: 0.4604 (OUTLIER) cc_final: 0.3913 (tmm) outliers start: 27 outliers final: 17 residues processed: 84 average time/residue: 0.1759 time to fit residues: 21.8596 Evaluate side-chains 79 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 406 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 0.0170 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 ASN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9018 Z= 0.187 Angle : 0.603 9.744 12613 Z= 0.330 Chirality : 0.042 0.166 1383 Planarity : 0.005 0.053 1288 Dihedral : 24.939 148.224 1975 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.17 % Favored : 94.70 % Rotamer: Outliers : 3.16 % Allowed : 18.27 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.27 (0.30), residues: 812 helix: -0.33 (0.31), residues: 302 sheet: 0.32 (0.57), residues: 87 loop : -1.48 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 264 HIS 0.004 0.001 HIS A 110 PHE 0.016 0.002 PHE B 109 TYR 0.013 0.001 TYR A 278 ARG 0.002 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 0.800 Fit side-chains REVERT: A 338 HIS cc_start: 0.5858 (p90) cc_final: 0.4221 (m-70) REVERT: A 403 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6933 (tppt) REVERT: B 110 HIS cc_start: 0.8369 (t-90) cc_final: 0.7836 (t70) REVERT: B 202 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5015 (t80) outliers start: 23 outliers final: 14 residues processed: 87 average time/residue: 0.1780 time to fit residues: 22.5788 Evaluate side-chains 78 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 403 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9018 Z= 0.323 Angle : 0.726 9.971 12613 Z= 0.393 Chirality : 0.046 0.183 1383 Planarity : 0.006 0.051 1288 Dihedral : 25.062 147.815 1975 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.85 % Allowed : 19.64 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.73 (0.29), residues: 812 helix: -0.79 (0.29), residues: 306 sheet: 0.12 (0.59), residues: 85 loop : -1.69 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 264 HIS 0.006 0.001 HIS A 137 PHE 0.030 0.003 PHE A 219 TYR 0.025 0.002 TYR B 17 ARG 0.003 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 59 time to evaluate : 0.888 Fit side-chains REVERT: B 110 HIS cc_start: 0.8560 (t-90) cc_final: 0.8175 (t-90) REVERT: B 202 TYR cc_start: 0.6324 (OUTLIER) cc_final: 0.5344 (t80) REVERT: B 289 ILE cc_start: 0.6909 (tt) cc_final: 0.6480 (tt) outliers start: 28 outliers final: 21 residues processed: 83 average time/residue: 0.1816 time to fit residues: 22.1160 Evaluate side-chains 79 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9018 Z= 0.254 Angle : 0.654 10.405 12613 Z= 0.356 Chirality : 0.044 0.185 1383 Planarity : 0.005 0.052 1288 Dihedral : 24.957 147.746 1975 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.30 % Allowed : 21.02 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.29), residues: 812 helix: -0.59 (0.30), residues: 302 sheet: 0.23 (0.57), residues: 85 loop : -1.64 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 264 HIS 0.005 0.001 HIS A 137 PHE 0.018 0.003 PHE B 109 TYR 0.021 0.002 TYR B 17 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 0.806 Fit side-chains REVERT: A 403 LYS cc_start: 0.7717 (pttt) cc_final: 0.7450 (pttm) REVERT: B 110 HIS cc_start: 0.8505 (t-90) cc_final: 0.8163 (t-90) REVERT: B 202 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5243 (t80) REVERT: B 289 ILE cc_start: 0.6738 (tt) cc_final: 0.6336 (tt) REVERT: B 393 ARG cc_start: 0.6185 (pmt170) cc_final: 0.5753 (ptt-90) outliers start: 24 outliers final: 21 residues processed: 84 average time/residue: 0.2046 time to fit residues: 24.5820 Evaluate side-chains 82 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 214 ASN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9018 Z= 0.190 Angle : 0.595 10.883 12613 Z= 0.323 Chirality : 0.041 0.153 1383 Planarity : 0.005 0.053 1288 Dihedral : 24.770 148.992 1975 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.57 % Allowed : 21.02 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.29 (0.30), residues: 812 helix: -0.35 (0.31), residues: 306 sheet: 0.30 (0.54), residues: 94 loop : -1.53 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 264 HIS 0.004 0.001 HIS A 110 PHE 0.020 0.002 PHE B 109 TYR 0.013 0.001 TYR A 157 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 69 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 338 HIS cc_start: 0.6012 (p90) cc_final: 0.4467 (m-70) REVERT: A 403 LYS cc_start: 0.7597 (pttt) cc_final: 0.6950 (tppt) REVERT: B 110 HIS cc_start: 0.8424 (t-90) cc_final: 0.8045 (t-90) REVERT: B 202 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.5074 (t80) REVERT: B 289 ILE cc_start: 0.6595 (tt) cc_final: 0.6192 (tt) outliers start: 26 outliers final: 21 residues processed: 90 average time/residue: 0.1846 time to fit residues: 24.3068 Evaluate side-chains 88 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 0.0070 chunk 58 optimal weight: 5.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9018 Z= 0.203 Angle : 0.606 10.049 12613 Z= 0.328 Chirality : 0.042 0.185 1383 Planarity : 0.005 0.052 1288 Dihedral : 24.734 149.057 1975 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.16 % Favored : 93.72 % Rotamer: Outliers : 4.12 % Allowed : 21.02 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.26 (0.30), residues: 812 helix: -0.32 (0.31), residues: 305 sheet: 0.40 (0.55), residues: 92 loop : -1.53 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 264 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE B 109 TYR 0.014 0.001 TYR B 17 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.5413 (ptp) REVERT: A 338 HIS cc_start: 0.5917 (p90) cc_final: 0.5693 (p-80) REVERT: A 403 LYS cc_start: 0.7655 (pttt) cc_final: 0.7017 (tppt) REVERT: B 110 HIS cc_start: 0.8469 (t-90) cc_final: 0.8142 (t-90) REVERT: B 202 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.5081 (t80) REVERT: B 289 ILE cc_start: 0.6616 (tt) cc_final: 0.6213 (tt) REVERT: B 393 ARG cc_start: 0.6175 (pmt170) cc_final: 0.5835 (ptt-90) outliers start: 30 outliers final: 26 residues processed: 89 average time/residue: 0.2161 time to fit residues: 27.3631 Evaluate side-chains 92 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 64 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 240 TYR Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 0.0060 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9018 Z= 0.307 Angle : 0.708 10.473 12613 Z= 0.381 Chirality : 0.045 0.206 1383 Planarity : 0.005 0.050 1288 Dihedral : 24.849 148.064 1975 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.12 % Allowed : 21.57 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: -1.67 (0.29), residues: 812 helix: -0.74 (0.29), residues: 304 sheet: 0.08 (0.54), residues: 97 loop : -1.69 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 264 HIS 0.006 0.001 HIS A 137 PHE 0.022 0.003 PHE B 352 TYR 0.027 0.002 TYR B 17 ARG 0.003 0.001 ARG B 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 57 time to evaluate : 0.906 Fit side-chains REVERT: A 123 GLN cc_start: 0.6625 (tp-100) cc_final: 0.6020 (pt0) REVERT: A 132 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5749 (ptp) REVERT: A 338 HIS cc_start: 0.6028 (p90) cc_final: 0.5755 (p90) REVERT: B 110 HIS cc_start: 0.8544 (t-90) cc_final: 0.8242 (t-90) REVERT: B 202 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5343 (t80) REVERT: B 393 ARG cc_start: 0.6254 (pmt170) cc_final: 0.5851 (ptt-90) outliers start: 30 outliers final: 26 residues processed: 80 average time/residue: 0.1984 time to fit residues: 22.8248 Evaluate side-chains 84 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 56 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 11 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.0020 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.132415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109168 restraints weight = 23973.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.111172 restraints weight = 14846.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.112603 restraints weight = 10285.002| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9018 Z= 0.158 Angle : 0.577 10.509 12613 Z= 0.313 Chirality : 0.040 0.176 1383 Planarity : 0.005 0.053 1288 Dihedral : 24.553 149.444 1975 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.43 % Allowed : 21.84 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.30), residues: 812 helix: -0.23 (0.31), residues: 310 sheet: 0.24 (0.55), residues: 92 loop : -1.50 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 264 HIS 0.006 0.001 HIS A 328 PHE 0.019 0.001 PHE B 109 TYR 0.012 0.001 TYR B 21 ARG 0.003 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.51 seconds wall clock time: 30 minutes 33.70 seconds (1833.70 seconds total)