Starting phenix.real_space_refine (version: 1.20rc2) on Mon Nov 1 17:04:22 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/11_2021/7sde_23517_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/11_2021/7sde_23517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/11_2021/7sde_23517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/11_2021/7sde_23517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/11_2021/7sde_23517_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sde_23517/11_2021/7sde_23517_neut.pdb" } resolution = 3.2 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc2-4405/modules/chem_data/mon_lib" Total number of atoms: 5734 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3856 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain breaks: 5 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 3.53, per 1000 atoms: 0.62 Number of scatterers: 5734 At special positions: 0 Unit cell: (68.096, 80.864, 105.336, 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 32 16.00 O 1011 8.00 N 943 7.00 C 3748 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 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 784.5 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1414 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 61.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.660A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.793A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.971A pdb=" N VAL A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.030A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.775A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.502A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 261 removed outlier: 3.920A pdb=" N CYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 292 through 302 removed outlier: 4.036A pdb=" N SER A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 4.481A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.936A pdb=" N PHE A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.565A pdb=" N THR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.918A pdb=" N LEU A 442 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.540A pdb=" N PHE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.950A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 4.087A pdb=" N ILE A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 518 through 529 removed outlier: 4.073A pdb=" N ARG A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 529 " --> pdb=" O TRP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 3.505A pdb=" N GLN A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.513A pdb=" N MET B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.541A pdb=" N ARG B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 354 through 366 removed outlier: 4.065A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.663A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.753A pdb=" N CYS B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 4.018A pdb=" N LEU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 2.42 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: 1785 1.34 - 1.46: 1133 1.46 - 1.58: 2893 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 5856 Sorted by residual: bond pdb=" CA GLU A 193 " pdb=" C GLU A 193 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.24e-02 6.50e+03 6.64e+00 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.25e-02 6.40e+03 3.33e+00 bond pdb=" N TYR A 20 " pdb=" CA TYR A 20 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.31e+00 bond pdb=" C MET A 241 " pdb=" O MET A 241 " ideal model delta sigma weight residual 1.244 1.226 0.018 1.00e-02 1.00e+04 3.15e+00 bond pdb=" CA ALA B 323 " pdb=" C ALA B 323 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.23e-02 6.61e+03 2.58e+00 ... (remaining 5851 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.90: 147 106.90 - 113.71: 3198 113.71 - 120.53: 2246 120.53 - 127.34: 2288 127.34 - 134.16: 41 Bond angle restraints: 7920 Sorted by residual: angle pdb=" N LYS A 146 " pdb=" CA LYS A 146 " pdb=" C LYS A 146 " ideal model delta sigma weight residual 110.24 123.45 -13.21 1.47e+00 4.63e-01 8.07e+01 angle pdb=" N GLN A 194 " pdb=" CA GLN A 194 " pdb=" C GLN A 194 " ideal model delta sigma weight residual 112.57 119.12 -6.55 1.13e+00 7.83e-01 3.36e+01 angle pdb=" N ARG A 364 " pdb=" CA ARG A 364 " pdb=" C ARG A 364 " ideal model delta sigma weight residual 113.12 106.11 7.01 1.25e+00 6.40e-01 3.15e+01 angle pdb=" C ASP A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 119.24 124.34 -5.10 1.04e+00 9.25e-01 2.40e+01 angle pdb=" N LYS A 146 " pdb=" CA LYS A 146 " pdb=" CB LYS A 146 " ideal model delta sigma weight residual 109.48 102.06 7.42 1.55e+00 4.16e-01 2.29e+01 ... (remaining 7915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3072 17.64 - 35.28: 307 35.28 - 52.92: 102 52.92 - 70.56: 28 70.56 - 88.20: 7 Dihedral angle restraints: 3516 sinusoidal: 1356 harmonic: 2160 Sorted by residual: dihedral pdb=" N TYR A 20 " pdb=" C TYR A 20 " pdb=" CA TYR A 20 " pdb=" CB TYR A 20 " ideal model delta harmonic sigma weight residual 122.80 135.03 -12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" C TYR A 20 " pdb=" N TYR A 20 " pdb=" CA TYR A 20 " pdb=" CB TYR A 20 " ideal model delta harmonic sigma weight residual -122.60 -134.70 12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" CA GLU B 398 " pdb=" C GLU B 398 " pdb=" N PHE B 399 " pdb=" CA PHE B 399 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 3513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 847 0.098 - 0.195: 52 0.195 - 0.293: 9 0.293 - 0.390: 2 0.390 - 0.488: 1 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA TYR A 20 " pdb=" N TYR A 20 " pdb=" C TYR A 20 " pdb=" CB TYR A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA TRP A 240 " pdb=" N TRP A 240 " pdb=" C TRP A 240 " pdb=" CB TRP A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 908 not shown) Planarity restraints: 993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 279 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C SER A 279 " 0.040 2.00e-02 2.50e+03 pdb=" O SER A 279 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO A 280 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 193 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU A 193 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 193 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 411 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C SER A 411 " 0.029 2.00e-02 2.50e+03 pdb=" O SER A 411 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 412 " -0.010 2.00e-02 2.50e+03 ... (remaining 990 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 591 2.74 - 3.28: 5984 3.28 - 3.82: 8827 3.82 - 4.36: 11087 4.36 - 4.90: 18709 Nonbonded interactions: 45198 Sorted by model distance: nonbonded pdb=" O SER A 458 " pdb=" OG SER A 458 " model vdw 2.201 2.440 nonbonded pdb=" O PHE A 461 " pdb=" NH2 ARG A 522 " model vdw 2.213 2.520 nonbonded pdb=" N GLU A 473 " pdb=" OE1 GLU A 473 " model vdw 2.216 2.520 nonbonded pdb=" O PHE A 50 " pdb=" NE2 GLN A 54 " model vdw 2.232 2.520 nonbonded pdb=" CD2 LEU A 438 " pdb=" OE1 GLU A 451 " model vdw 2.278 3.460 ... (remaining 45193 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 3748 2.51 5 N 943 2.21 5 O 1011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.190 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 18.580 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.250 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 27.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5856 Z= 0.239 Angle : 0.918 13.208 7920 Z= 0.621 Chirality : 0.057 0.488 911 Planarity : 0.003 0.037 993 Dihedral : 17.029 88.204 2102 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.62 % Favored : 89.09 % Rotamer Outliers : 8.60 % Cbeta Deviations : 0.14 % 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: -4.65 (0.25), residues: 706 helix: -2.68 (0.21), residues: 412 sheet: None (None), residues: 0 loop : -3.61 (0.29), residues: 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 116 time to evaluate : 0.664 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 29 residues processed: 157 average time/residue: 0.1801 time to fit residues: 36.4711 Evaluate side-chains 118 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.0882 time to fit residues: 4.7802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS A 90 ASN A 94 ASN A 134 GLN A 227 GLN A 274 GLN A 292 ASN A 345 GLN A 383 GLN A 495 HIS B 201 HIS B 206 ASN B 211 GLN B 389 GLN B 407 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5856 Z= 0.209 Angle : 0.600 8.854 7920 Z= 0.304 Chirality : 0.040 0.172 911 Planarity : 0.004 0.042 993 Dihedral : 4.447 21.252 771 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 0.99 % 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: -2.80 (0.29), residues: 706 helix: -0.99 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -3.31 (0.30), residues: 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.724 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 117 average time/residue: 0.1717 time to fit residues: 26.7158 Evaluate side-chains 99 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0610 time to fit residues: 1.4279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5856 Z= 0.193 Angle : 0.564 7.520 7920 Z= 0.280 Chirality : 0.039 0.127 911 Planarity : 0.004 0.045 993 Dihedral : 4.227 18.452 771 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 2.64 % 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: -1.75 (0.31), residues: 706 helix: -0.11 (0.26), residues: 439 sheet: None (None), residues: 0 loop : -2.99 (0.32), residues: 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.731 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 114 average time/residue: 0.1790 time to fit residues: 26.9899 Evaluate side-chains 96 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0641 time to fit residues: 1.6609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5856 Z= 0.203 Angle : 0.592 10.459 7920 Z= 0.287 Chirality : 0.040 0.146 911 Planarity : 0.004 0.047 993 Dihedral : 4.200 19.868 771 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 1.98 % 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: -1.33 (0.31), residues: 706 helix: 0.23 (0.26), residues: 437 sheet: None (None), residues: 0 loop : -2.82 (0.32), residues: 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.758 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.1756 time to fit residues: 25.0679 Evaluate side-chains 98 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0540 time to fit residues: 1.8237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 ASN B 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 5856 Z= 0.243 Angle : 0.609 14.115 7920 Z= 0.296 Chirality : 0.041 0.126 911 Planarity : 0.004 0.047 993 Dihedral : 4.335 20.017 771 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 1.98 % 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: -1.09 (0.31), residues: 706 helix: 0.32 (0.26), residues: 440 sheet: None (None), residues: 0 loop : -2.54 (0.34), residues: 266 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.735 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.1764 time to fit residues: 24.7551 Evaluate side-chains 95 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.724 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0645 time to fit residues: 1.9004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 5856 Z= 0.228 Angle : 0.596 14.032 7920 Z= 0.292 Chirality : 0.041 0.165 911 Planarity : 0.004 0.047 993 Dihedral : 4.266 20.346 771 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 1.65 % 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: -0.93 (0.32), residues: 706 helix: 0.42 (0.26), residues: 440 sheet: None (None), residues: 0 loop : -2.44 (0.34), residues: 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.667 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.1703 time to fit residues: 22.7563 Evaluate side-chains 91 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0577 time to fit residues: 1.6969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 5856 Z= 0.200 Angle : 0.596 12.868 7920 Z= 0.286 Chirality : 0.040 0.188 911 Planarity : 0.004 0.049 993 Dihedral : 4.171 20.666 771 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 1.16 % 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: -0.71 (0.32), residues: 706 helix: 0.63 (0.26), residues: 437 sheet: None (None), residues: 0 loop : -2.38 (0.34), residues: 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 0.1746 time to fit residues: 24.8609 Evaluate side-chains 92 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.733 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0653 time to fit residues: 1.3323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 GLN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.143 5856 Z= 0.218 Angle : 0.645 15.045 7920 Z= 0.306 Chirality : 0.041 0.184 911 Planarity : 0.005 0.116 993 Dihedral : 4.043 20.926 771 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer Outliers : 0.83 % 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 (0.32), residues: 706 helix: 0.85 (0.26), residues: 433 sheet: None (None), residues: 0 loop : -2.22 (0.35), residues: 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 99 average time/residue: 0.1781 time to fit residues: 23.4359 Evaluate side-chains 93 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0572 time to fit residues: 1.3729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 63 optimal weight: 0.0670 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 65 optimal weight: 0.4980 chunk 56 optimal weight: 0.0020 overall best weight: 0.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.157 5856 Z= 0.208 Angle : 0.630 14.615 7920 Z= 0.303 Chirality : 0.039 0.180 911 Planarity : 0.005 0.124 993 Dihedral : 3.745 20.654 771 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.33), residues: 706 helix: 1.17 (0.27), residues: 432 sheet: None (None), residues: 0 loop : -1.95 (0.36), residues: 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.691 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.1920 time to fit residues: 26.7510 Evaluate side-chains 95 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.711 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 0.0000 chunk 8 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.174 5856 Z= 0.257 Angle : 0.695 15.801 7920 Z= 0.347 Chirality : 0.041 0.179 911 Planarity : 0.006 0.140 993 Dihedral : 3.913 20.350 771 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer Outliers : 0.50 % 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: -0.01 (0.33), residues: 706 helix: 1.17 (0.26), residues: 431 sheet: None (None), residues: 0 loop : -1.99 (0.36), residues: 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.761 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 92 average time/residue: 0.1821 time to fit residues: 22.2103 Evaluate side-chains 89 residues out of total 680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0756 time to fit residues: 1.3082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.181975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.155331 restraints weight = 7444.383| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.70 r_work: 0.3926 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work: 0.3892 rms_B_bonded: 1.77 restraints_weight: 0.1250 r_work: 0.3867 rms_B_bonded: 2.10 restraints_weight: 0.0625 r_work: 0.3834 rms_B_bonded: 2.64 restraints_weight: 0.0312 r_work: 0.3784 rms_B_bonded: 3.54 restraints_weight: 0.0156 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.169 5856 Z= 0.294 Angle : 0.729 16.389 7920 Z= 0.363 Chirality : 0.043 0.182 911 Planarity : 0.006 0.144 993 Dihedral : 4.260 20.165 771 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer Outliers : 0.17 % 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: -0.25 (0.32), residues: 706 helix: 0.97 (0.26), residues: 427 sheet: None (None), residues: 0 loop : -2.02 (0.35), residues: 279 =============================================================================== Job complete usr+sys time: 1376.97 seconds wall clock time: 25 minutes 48.82 seconds (1548.82 seconds total)