Starting phenix.real_space_refine on Tue Nov 14 11:49:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/11_2023/7zla_14778_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/11_2023/7zla_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_14778/11_2023/7zla_14778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/11_2023/7zla_14778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/11_2023/7zla_14778_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zla_14778/11_2023/7zla_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-1.21rc1-5144/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: 5.09, per 1000 atoms: 0.59 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: 4.26 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: 3.90 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: 2.53 Time building geometry restraints manager: 4.45 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 1.726 1.547 0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.548 0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.437 -0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.434 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" C4 LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.464 1.617 -0.153 2.00e-02 2.50e+03 5.87e+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 120.09 109.59 10.50 3.00e+00 1.11e-01 1.22e+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 120.09 110.13 9.96 3.00e+00 1.11e-01 1.10e+01 ... (remaining 12608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 4512 29.58 - 59.16: 504 59.16 - 88.73: 33 88.73 - 118.31: 1 118.31 - 147.89: 4 Dihedral angle restraints: 5054 sinusoidal: 2626 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 5051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 963 0.045 - 0.090: 316 0.090 - 0.136: 91 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: 0.820 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: 0.000 Extract box with map and model: 4.060 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.730 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- 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 : 0.007 0.179 9018 Z= 0.471 Angle : 0.860 10.499 12613 Z= 0.483 Chirality : 0.048 0.226 1383 Planarity : 0.010 0.296 1288 Dihedral : 21.490 147.890 3498 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 *********************** 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 : 0.818 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1877 time to fit residues: 23.8961 Evaluate side-chains 57 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1706 ------------------------------------------------------------------------------- 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: 0.4980 chunk 69 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6671 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9018 Z= 0.244 Angle : 0.664 9.573 12613 Z= 0.364 Chirality : 0.044 0.155 1383 Planarity : 0.005 0.052 1288 Dihedral : 24.504 148.191 1849 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.24 % Allowed : 7.97 % Favored : 90.80 % 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: -1.55 (0.28), residues: 812 helix: -0.76 (0.29), residues: 309 sheet: -0.22 (0.54), residues: 86 loop : -1.37 (0.29), residues: 417 *********************** 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 75 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.909 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.1865 time to fit residues: 20.0013 Evaluate side-chains 64 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.854 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0830 time to fit residues: 2.0236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** 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: 0.6736 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9018 Z= 0.289 Angle : 0.700 9.332 12613 Z= 0.378 Chirality : 0.045 0.162 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.736 147.969 1849 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.06 % Allowed : 12.64 % Favored : 85.30 % 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: -1.57 (0.29), residues: 812 helix: -0.73 (0.29), residues: 309 sheet: 0.02 (0.55), residues: 87 loop : -1.50 (0.30), residues: 416 *********************** 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 80 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.939 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 76 average time/residue: 0.1889 time to fit residues: 21.0346 Evaluate side-chains 62 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1307 time to fit residues: 2.3604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 71 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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: 0.6780 moved from start: 0.1968 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= 0.312 Angle : 0.721 9.217 12613 Z= 0.391 Chirality : 0.046 0.174 1383 Planarity : 0.005 0.050 1288 Dihedral : 24.924 147.191 1849 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.06 % Allowed : 17.86 % Favored : 80.08 % 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: -1.72 (0.29), residues: 812 helix: -0.89 (0.29), residues: 309 sheet: 0.13 (0.58), residues: 85 loop : -1.59 (0.30), residues: 418 *********************** 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 77 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.849 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.1791 time to fit residues: 19.5329 Evaluate side-chains 63 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0829 time to fit residues: 2.2559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.4980 chunk 64 optimal weight: 0.0170 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.2220 ------------------------------------------------------------------------------- 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 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9018 Z= 0.176 Angle : 0.587 9.746 12613 Z= 0.322 Chirality : 0.041 0.161 1383 Planarity : 0.005 0.052 1288 Dihedral : 24.682 147.984 1849 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.93 % Favored : 94.95 % Rotamer: Outliers : 1.24 % Allowed : 17.86 % Favored : 80.91 % 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 (0.29), residues: 812 helix: -0.45 (0.31), residues: 311 sheet: 0.45 (0.55), residues: 91 loop : -1.43 (0.30), residues: 410 *********************** 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 77 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.791 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 77 average time/residue: 0.1783 time to fit residues: 20.2150 Evaluate side-chains 63 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0794 time to fit residues: 1.4944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 145 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9018 Z= 0.381 Angle : 0.780 9.427 12613 Z= 0.421 Chirality : 0.048 0.189 1383 Planarity : 0.006 0.050 1288 Dihedral : 25.059 147.306 1849 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.51 % Allowed : 20.19 % Favored : 78.30 % 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: -1.80 (0.29), residues: 812 helix: -0.95 (0.29), residues: 299 sheet: 0.28 (0.59), residues: 85 loop : -1.69 (0.29), residues: 428 *********************** 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 70 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.838 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.1757 time to fit residues: 17.3944 Evaluate side-chains 64 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0840 time to fit residues: 1.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 62 GLN ** B 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9018 Z= 0.168 Angle : 0.573 10.085 12613 Z= 0.315 Chirality : 0.040 0.160 1383 Planarity : 0.005 0.053 1288 Dihedral : 24.620 148.046 1849 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.68 % Favored : 95.20 % Rotamer: Outliers : 0.69 % Allowed : 20.74 % 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: -1.11 (0.30), residues: 812 helix: -0.33 (0.31), residues: 309 sheet: 0.52 (0.55), residues: 93 loop : -1.35 (0.31), residues: 410 *********************** 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 75 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.855 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 75 average time/residue: 0.1854 time to fit residues: 20.3226 Evaluate side-chains 64 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0800 time to fit residues: 1.2289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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 338 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: 0.6662 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9018 Z= 0.214 Angle : 0.616 9.944 12613 Z= 0.333 Chirality : 0.042 0.175 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.562 148.585 1849 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 1.51 % Allowed : 21.84 % Favored : 76.65 % 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: -1.15 (0.30), residues: 812 helix: -0.35 (0.30), residues: 307 sheet: 0.55 (0.55), residues: 92 loop : -1.37 (0.31), residues: 413 *********************** 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 78 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.890 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 74 average time/residue: 0.1864 time to fit residues: 20.6893 Evaluate side-chains 69 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0830 time to fit residues: 2.1005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 145 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: 0.6772 moved from start: 0.3055 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= 0.311 Angle : 0.719 12.063 12613 Z= 0.386 Chirality : 0.046 0.175 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.767 147.361 1849 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.69 % Allowed : 22.66 % Favored : 76.65 % 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: -1.62 (0.29), residues: 812 helix: -0.66 (0.30), residues: 298 sheet: 0.24 (0.55), residues: 92 loop : -1.70 (0.30), residues: 422 *********************** 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 69 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 67 average time/residue: 0.1970 time to fit residues: 19.4701 Evaluate side-chains 60 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0921 time to fit residues: 1.7646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9018 Z= 0.189 Angle : 0.607 12.008 12613 Z= 0.326 Chirality : 0.042 0.203 1383 Planarity : 0.005 0.053 1288 Dihedral : 24.453 147.963 1849 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.30 % Favored : 94.58 % Rotamer: Outliers : 0.55 % Allowed : 22.66 % Favored : 76.79 % 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: -0.25 (0.31), residues: 299 sheet: 0.71 (0.56), residues: 86 loop : -1.55 (0.30), residues: 427 ********************** 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 69 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.812 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.1922 time to fit residues: 19.0907 Evaluate side-chains 61 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0869 time to fit residues: 1.2559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 171 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.130636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.107774 restraints weight = 24222.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.109686 restraints weight = 14979.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.111130 restraints weight = 10530.239| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9018 Z= 0.211 Angle : 0.625 11.929 12613 Z= 0.336 Chirality : 0.042 0.197 1383 Planarity : 0.005 0.051 1288 Dihedral : 24.387 148.284 1849 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 0.82 % Allowed : 22.66 % 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: -1.16 (0.30), residues: 812 helix: -0.22 (0.31), residues: 296 sheet: 0.57 (0.55), residues: 91 loop : -1.48 (0.31), residues: 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.74 seconds wall clock time: 28 minutes 23.16 seconds (1703.16 seconds total)