Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 13:04:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/04_2023/6uz2_20950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/04_2023/6uz2_20950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/04_2023/6uz2_20950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/04_2023/6uz2_20950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/04_2023/6uz2_20950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uz2_20950/04_2023/6uz2_20950.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4640 2.51 5 N 1328 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 7392 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3694 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'PTRANS': 13, 'TRANS': 556} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 749 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 21, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 434 Chain: "B" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3698 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PTRANS': 13, 'TRANS': 556} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 954 Unresolved non-hydrogen dihedrals: 585 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 430 Time building chain proxies: 4.64, per 1000 atoms: 0.63 Number of scatterers: 7392 At special positions: 0 Unit cell: (72, 96, 131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1380 8.00 N 1328 7.00 C 4640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 71.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 24 through 47 Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.574A pdb=" N ASP A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 62 through 109 removed outlier: 3.712A pdb=" N TRP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 120 through 164 removed outlier: 3.556A pdb=" N GLY A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 196 Proline residue: A 176 - end of helix removed outlier: 3.755A pdb=" N MET A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 221 removed outlier: 5.028A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 269 removed outlier: 3.553A pdb=" N LYS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.640A pdb=" N ALA A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 280 through 324 Proline residue: A 297 - end of helix removed outlier: 4.073A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.834A pdb=" N ALA A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.687A pdb=" N ASP A 471 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 512 through 527 Processing helix chain 'A' and resid 538 through 545 removed outlier: 4.118A pdb=" N ALA A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.521A pdb=" N ALA A 573 " --> pdb=" O GLY A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 18 through 22 Proline residue: B 22 - end of helix Processing helix chain 'B' and resid 23 through 53 removed outlier: 3.861A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 60 through 109 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 120 through 164 Processing helix chain 'B' and resid 164 through 213 Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 222 through 275 removed outlier: 4.767A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 280 through 323 removed outlier: 3.632A pdb=" N PHE B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.797A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLN B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.668A pdb=" N ASN B 464 " --> pdb=" O MET B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 512 through 527 Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.677A pdb=" N LYS B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA B 545 " --> pdb=" O THR B 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.590A pdb=" N GLN B 574 " --> pdb=" O GLY B 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366 removed outlier: 5.615A pdb=" N ARG A 360 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 349 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 364 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ARG A 345 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 366 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU A 343 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL A 347 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU A 397 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 374 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 422 removed outlier: 5.311A pdb=" N ALA A 420 " --> pdb=" O ILE A 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422 removed outlier: 3.653A pdb=" N VAL B 422 " --> pdb=" O ILE B 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 586 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2498 1.34 - 1.45: 996 1.45 - 1.57: 3894 1.57 - 1.69: 2 1.69 - 1.81: 84 Bond restraints: 7474 Sorted by residual: bond pdb=" CG ARG B 296 " pdb=" CD ARG B 296 " ideal model delta sigma weight residual 1.520 1.588 -0.068 3.00e-02 1.11e+03 5.18e+00 bond pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " ideal model delta sigma weight residual 1.520 1.588 -0.068 3.00e-02 1.11e+03 5.15e+00 bond pdb=" CB TRP A 17 " pdb=" CG TRP A 17 " ideal model delta sigma weight residual 1.498 1.436 0.062 3.10e-02 1.04e+03 4.02e+00 bond pdb=" CB PHE A 13 " pdb=" CG PHE A 13 " ideal model delta sigma weight residual 1.502 1.459 0.043 2.30e-02 1.89e+03 3.52e+00 bond pdb=" CB TRP B 17 " pdb=" CG TRP B 17 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.30e+00 ... (remaining 7469 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.43: 120 105.43 - 112.58: 4184 112.58 - 119.73: 2254 119.73 - 126.88: 3589 126.88 - 134.03: 48 Bond angle restraints: 10195 Sorted by residual: angle pdb=" N HIS B 537 " pdb=" CA HIS B 537 " pdb=" C HIS B 537 " ideal model delta sigma weight residual 112.59 100.04 12.55 1.22e+00 6.72e-01 1.06e+02 angle pdb=" C MET A 295 " pdb=" N ARG A 296 " pdb=" CA ARG A 296 " ideal model delta sigma weight residual 119.83 112.91 6.92 1.11e+00 8.12e-01 3.88e+01 angle pdb=" N ALA B 536 " pdb=" CA ALA B 536 " pdb=" C ALA B 536 " ideal model delta sigma weight residual 108.56 118.02 -9.46 1.74e+00 3.30e-01 2.95e+01 angle pdb=" N SER B 164 " pdb=" CA SER B 164 " pdb=" C SER B 164 " ideal model delta sigma weight residual 107.93 116.15 -8.22 1.65e+00 3.67e-01 2.48e+01 angle pdb=" N TYR A 163 " pdb=" CA TYR A 163 " pdb=" C TYR A 163 " ideal model delta sigma weight residual 111.36 116.32 -4.96 1.09e+00 8.42e-01 2.07e+01 ... (remaining 10190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.39: 3904 13.39 - 26.77: 398 26.77 - 40.16: 121 40.16 - 53.54: 39 53.54 - 66.93: 9 Dihedral angle restraints: 4471 sinusoidal: 1189 harmonic: 3282 Sorted by residual: dihedral pdb=" CA GLU A 552 " pdb=" C GLU A 552 " pdb=" N ASP A 553 " pdb=" CA ASP A 553 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ALA A 457 " pdb=" C ALA A 457 " pdb=" N TYR A 458 " pdb=" CA TYR A 458 " ideal model delta harmonic sigma weight residual 180.00 151.96 28.04 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS B 544 " pdb=" C LYS B 544 " pdb=" N ALA B 545 " pdb=" CA ALA B 545 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 4468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 883 0.048 - 0.096: 318 0.096 - 0.143: 73 0.143 - 0.191: 5 0.191 - 0.239: 5 Chirality restraints: 1284 Sorted by residual: chirality pdb=" CA VAL A 334 " pdb=" N VAL A 334 " pdb=" C VAL A 334 " pdb=" CB VAL A 334 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ALA B 536 " pdb=" N ALA B 536 " pdb=" C ALA B 536 " pdb=" CB ALA B 536 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA TYR A 163 " pdb=" N TYR A 163 " pdb=" C TYR A 163 " pdb=" CB TYR A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1281 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 262 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C ALA B 262 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA B 262 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 263 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 136 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ALA B 136 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA B 136 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 137 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 296 " 0.039 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO B 297 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 297 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 297 " 0.032 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1320 2.74 - 3.28: 8957 3.28 - 3.82: 12479 3.82 - 4.36: 13927 4.36 - 4.90: 22048 Nonbonded interactions: 58731 Sorted by model distance: nonbonded pdb=" O ARG A 78 " pdb=" OG1 THR A 81 " model vdw 2.197 2.440 nonbonded pdb=" O GLN B 256 " pdb=" OG SER B 260 " model vdw 2.200 2.440 nonbonded pdb=" O PRO A 297 " pdb=" OG SER A 300 " model vdw 2.201 2.440 nonbonded pdb=" O ALA A 175 " pdb=" OG SER A 179 " model vdw 2.202 2.440 nonbonded pdb=" O VAL A 135 " pdb=" OG SER A 139 " model vdw 2.208 2.440 ... (remaining 58726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or resid 150 through 580)) } 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: 0.730 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: 4.270 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.380 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.068 7474 Z= 0.574 Angle : 1.131 13.667 10195 Z= 0.668 Chirality : 0.051 0.239 1284 Planarity : 0.005 0.057 1327 Dihedral : 13.781 66.927 2339 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.49 % Favored : 84.33 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.18), residues: 1136 helix: -3.00 (0.14), residues: 715 sheet: -3.18 (0.60), residues: 43 loop : -4.28 (0.25), residues: 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 252 average time/residue: 0.1915 time to fit residues: 64.1710 Evaluate side-chains 183 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0670 time to fit residues: 1.7807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 chunk 34 optimal weight: 0.0000 chunk 54 optimal weight: 50.0000 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 30.0000 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7474 Z= 0.253 Angle : 0.717 9.010 10195 Z= 0.382 Chirality : 0.045 0.174 1284 Planarity : 0.005 0.052 1327 Dihedral : 5.462 24.254 1184 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.52 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.23), residues: 1136 helix: -0.97 (0.17), residues: 750 sheet: -3.14 (0.76), residues: 39 loop : -3.40 (0.30), residues: 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 252 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.1498 time to fit residues: 53.9446 Evaluate side-chains 187 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 40.0000 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 83 optimal weight: 0.0070 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS B 119 GLN B 326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7474 Z= 0.202 Angle : 0.646 8.015 10195 Z= 0.343 Chirality : 0.044 0.131 1284 Planarity : 0.004 0.042 1327 Dihedral : 4.855 19.463 1184 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.24), residues: 1136 helix: 0.05 (0.18), residues: 762 sheet: -2.50 (0.97), residues: 27 loop : -3.05 (0.32), residues: 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 250 average time/residue: 0.1621 time to fit residues: 57.1434 Evaluate side-chains 198 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 40.0000 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 98 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7474 Z= 0.214 Angle : 0.618 9.131 10195 Z= 0.331 Chirality : 0.043 0.146 1284 Planarity : 0.004 0.042 1327 Dihedral : 4.546 19.113 1184 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.25), residues: 1136 helix: 0.51 (0.19), residues: 767 sheet: -4.34 (0.78), residues: 15 loop : -2.75 (0.33), residues: 354 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.1593 time to fit residues: 55.9502 Evaluate side-chains 190 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 56 optimal weight: 40.0000 chunk 98 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7474 Z= 0.184 Angle : 0.609 7.662 10195 Z= 0.319 Chirality : 0.043 0.144 1284 Planarity : 0.003 0.040 1327 Dihedral : 4.271 18.530 1184 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.26), residues: 1136 helix: 0.89 (0.19), residues: 771 sheet: -3.56 (0.68), residues: 25 loop : -2.59 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1523 time to fit residues: 54.0658 Evaluate side-chains 192 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 40.0000 chunk 57 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7474 Z= 0.278 Angle : 0.665 6.996 10195 Z= 0.358 Chirality : 0.044 0.161 1284 Planarity : 0.004 0.049 1327 Dihedral : 4.382 22.436 1184 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1136 helix: 0.79 (0.19), residues: 752 sheet: -2.64 (0.69), residues: 35 loop : -2.43 (0.35), residues: 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1628 time to fit residues: 54.1372 Evaluate side-chains 184 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 50.0000 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 50.0000 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7474 Z= 0.199 Angle : 0.624 7.707 10195 Z= 0.328 Chirality : 0.043 0.179 1284 Planarity : 0.004 0.044 1327 Dihedral : 4.216 19.581 1184 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1136 helix: 0.99 (0.19), residues: 762 sheet: -2.51 (0.71), residues: 35 loop : -2.36 (0.37), residues: 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1504 time to fit residues: 49.5467 Evaluate side-chains 182 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 40.0000 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 54 optimal weight: 50.0000 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7474 Z= 0.239 Angle : 0.662 9.291 10195 Z= 0.351 Chirality : 0.044 0.165 1284 Planarity : 0.004 0.036 1327 Dihedral : 4.284 24.933 1184 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1136 helix: 0.97 (0.19), residues: 768 sheet: -2.30 (0.74), residues: 35 loop : -2.33 (0.37), residues: 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1414 time to fit residues: 45.7974 Evaluate side-chains 180 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 50.0000 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN B 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 7474 Z= 0.304 Angle : 0.731 9.212 10195 Z= 0.389 Chirality : 0.046 0.211 1284 Planarity : 0.004 0.036 1327 Dihedral : 4.457 25.297 1184 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1136 helix: 0.81 (0.19), residues: 774 sheet: -2.61 (0.64), residues: 50 loop : -2.25 (0.38), residues: 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1428 time to fit residues: 44.4760 Evaluate side-chains 170 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 104 optimal weight: 10.0000 chunk 90 optimal weight: 50.0000 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7474 Z= 0.222 Angle : 0.675 8.405 10195 Z= 0.356 Chirality : 0.044 0.173 1284 Planarity : 0.004 0.040 1327 Dihedral : 4.313 25.861 1184 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1136 helix: 0.97 (0.19), residues: 775 sheet: -2.26 (0.68), residues: 55 loop : -2.17 (0.39), residues: 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1484 time to fit residues: 46.8211 Evaluate side-chains 180 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0370 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 40.0000 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.0470 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** 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 = 0.3928 r_free = 0.3928 target = 0.119053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095767 restraints weight = 23985.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.098040 restraints weight = 14983.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.099676 restraints weight = 10431.520| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7474 Z= 0.208 Angle : 0.690 11.093 10195 Z= 0.362 Chirality : 0.045 0.181 1284 Planarity : 0.004 0.042 1327 Dihedral : 4.270 23.897 1184 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.27), residues: 1136 helix: 1.02 (0.19), residues: 781 sheet: -2.23 (0.68), residues: 55 loop : -2.17 (0.40), residues: 300 =============================================================================== Job complete usr+sys time: 1669.23 seconds wall clock time: 30 minutes 47.99 seconds (1847.99 seconds total)