Starting phenix.real_space_refine on Sun Apr 7 03:45:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/04_2024/8thi_41265_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/04_2024/8thi_41265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/04_2024/8thi_41265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/04_2024/8thi_41265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/04_2024/8thi_41265_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/04_2024/8thi_41265_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 Na 2 4.78 5 C 6392 2.51 5 N 1464 2.21 5 O 1593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 480": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9519 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4739 Classifications: {'peptide': 613} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 586} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4719 Classifications: {'peptide': 611} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 584} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' NA': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' NA': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Time building chain proxies: 5.39, per 1000 atoms: 0.57 Number of scatterers: 9519 At special positions: 0 Unit cell: (73.04, 88.312, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 2 15.00 Na 2 11.00 O 1593 8.00 N 1464 7.00 C 6392 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: 3.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 40 through 62 removed outlier: 3.757A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 77 through 107 removed outlier: 4.445A pdb=" N PHE A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 removed outlier: 4.492A pdb=" N ALA A 127 " --> pdb=" O TRP A 123 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.724A pdb=" N LEU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.733A pdb=" N PHE A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 178 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 179 " --> pdb=" O TRP A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 179' Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.222A pdb=" N PHE A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 241 removed outlier: 4.382A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.678A pdb=" N VAL A 249 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.668A pdb=" N GLY A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 removed outlier: 3.592A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.891A pdb=" N CYS A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLY A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 357 through 386 removed outlier: 4.435A pdb=" N ILE A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 396 through 421 removed outlier: 5.324A pdb=" N TRP A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 451 through 484 removed outlier: 3.969A pdb=" N VAL A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 502 through 518 removed outlier: 3.860A pdb=" N MET A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 539 removed outlier: 3.786A pdb=" N PHE A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Proline residue: A 531 - end of helix Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 544 through 560 removed outlier: 3.583A pdb=" N GLY A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A 560 " --> pdb=" O MET A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 579 through 602 Proline residue: A 588 - end of helix removed outlier: 4.676A pdb=" N ILE A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 604 through 614 removed outlier: 4.599A pdb=" N VAL A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Proline residue: A 611 - end of helix Processing helix chain 'B' and resid 7 through 31 Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.799A pdb=" N TYR B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 77 through 108 removed outlier: 3.692A pdb=" N PHE B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 122 through 148 removed outlier: 4.547A pdb=" N ALA B 127 " --> pdb=" O TRP B 123 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Proline residue: B 129 - end of helix removed outlier: 3.716A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.725A pdb=" N VAL B 179 " --> pdb=" O TRP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 190 through 206 removed outlier: 3.692A pdb=" N VAL B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE B 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.251A pdb=" N PHE B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 removed outlier: 4.721A pdb=" N GLU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL B 238 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 259 Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 262 through 276 Processing helix chain 'B' and resid 282 through 295 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'B' and resid 323 through 339 removed outlier: 3.912A pdb=" N CYS B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 357 through 386 removed outlier: 4.360A pdb=" N ILE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 396 through 422 removed outlier: 5.638A pdb=" N TRP B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 412 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 451 through 484 removed outlier: 4.054A pdb=" N VAL B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 500 removed outlier: 5.947A pdb=" N ALA B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL B 498 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 499 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 518 removed outlier: 3.961A pdb=" N MET B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 539 Proline residue: B 531 - end of helix Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 544 through 560 removed outlier: 3.658A pdb=" N GLY B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU B 560 " --> pdb=" O MET B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 575 Processing helix chain 'B' and resid 579 through 602 Proline residue: B 588 - end of helix removed outlier: 4.506A pdb=" N ILE B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 604 through 614 removed outlier: 4.340A pdb=" N VAL B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Proline residue: B 611 - end of helix 611 hydrogen bonds defined for protein. 1737 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: 2.53 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1427 1.32 - 1.44: 2580 1.44 - 1.56: 5611 1.56 - 1.69: 4 1.69 - 1.81: 122 Bond restraints: 9744 Sorted by residual: bond pdb=" N ILE A 4 " pdb=" CA ILE A 4 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.32e+01 bond pdb=" N THR A 280 " pdb=" CA THR A 280 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.19e+00 bond pdb=" N ASN A 5 " pdb=" CA ASN A 5 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.36e-02 5.41e+03 6.43e+00 bond pdb=" N LYS A 178 " pdb=" CA LYS A 178 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.31e-02 5.83e+03 6.36e+00 bond pdb=" N VAL B 498 " pdb=" CA VAL B 498 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.33e-02 5.65e+03 6.35e+00 ... (remaining 9739 not shown) Histogram of bond angle deviations from ideal: 92.06 - 100.46: 10 100.46 - 108.85: 398 108.85 - 117.25: 6609 117.25 - 125.65: 6095 125.65 - 134.04: 126 Bond angle restraints: 13238 Sorted by residual: angle pdb=" N VAL A 498 " pdb=" CA VAL A 498 " pdb=" C VAL A 498 " ideal model delta sigma weight residual 113.10 110.06 3.04 9.70e-01 1.06e+00 9.81e+00 angle pdb=" C GLY A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta sigma weight residual 120.31 115.67 4.64 1.52e+00 4.33e-01 9.33e+00 angle pdb=" N ASN A 5 " pdb=" CA ASN A 5 " pdb=" C ASN A 5 " ideal model delta sigma weight residual 114.04 110.50 3.54 1.24e+00 6.50e-01 8.16e+00 angle pdb=" CA ASP B 500 " pdb=" C ASP B 500 " pdb=" O ASP B 500 " ideal model delta sigma weight residual 121.07 117.93 3.14 1.10e+00 8.26e-01 8.14e+00 angle pdb=" N LYS A 178 " pdb=" CA LYS A 178 " pdb=" C LYS A 178 " ideal model delta sigma weight residual 113.18 109.97 3.21 1.21e+00 6.83e-01 7.06e+00 ... (remaining 13233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 5031 16.30 - 32.61: 529 32.61 - 48.91: 120 48.91 - 65.21: 23 65.21 - 81.51: 5 Dihedral angle restraints: 5708 sinusoidal: 2193 harmonic: 3515 Sorted by residual: dihedral pdb=" CB MET B 556 " pdb=" CG MET B 556 " pdb=" SD MET B 556 " pdb=" CE MET B 556 " ideal model delta sinusoidal sigma weight residual 60.00 114.20 -54.20 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CB LYS B 236 " pdb=" CG LYS B 236 " pdb=" CD LYS B 236 " pdb=" CE LYS B 236 " ideal model delta sinusoidal sigma weight residual -60.00 -114.11 54.11 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CB MET A 556 " pdb=" CG MET A 556 " pdb=" SD MET A 556 " pdb=" CE MET A 556 " ideal model delta sinusoidal sigma weight residual 60.00 114.10 -54.10 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1255 0.046 - 0.091: 299 0.091 - 0.137: 45 0.137 - 0.183: 1 0.183 - 0.229: 3 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL B 498 " pdb=" CA VAL B 498 " pdb=" CG1 VAL B 498 " pdb=" CG2 VAL B 498 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL B 498 " pdb=" N VAL B 498 " pdb=" C VAL B 498 " pdb=" CB VAL B 498 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 1600 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 281 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C GLY A 281 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY A 281 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY A 282 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 498 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL B 498 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 498 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 499 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 426 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 427 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.018 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1188 2.75 - 3.29: 9696 3.29 - 3.82: 15860 3.82 - 4.36: 17187 4.36 - 4.90: 31305 Nonbonded interactions: 75236 Sorted by model distance: nonbonded pdb=" O SER A 298 " pdb="NA NA A 702 " model vdw 2.209 2.470 nonbonded pdb=" O VAL B 179 " pdb=" OH TYR B 185 " model vdw 2.209 2.440 nonbonded pdb=" O GLY A 277 " pdb=" OG1 THR A 391 " model vdw 2.234 2.440 nonbonded pdb=" O THR B 450 " pdb=" OG SER B 453 " model vdw 2.281 2.440 nonbonded pdb=" O GLY A 337 " pdb="NA NA A 702 " model vdw 2.303 2.470 ... (remaining 75231 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' and (resid 5 through 615 or (resid 701 and (name C1 or name C11 or na \ me C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C4 or n \ ame C5 or name C6 or name O11 or name O1P or name O2 or name O2P or name O3 or n \ ame O31 or name O3P or name O4P or name O5 or name O6 or name P )) or resid 702) \ ) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.440 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: 0.020 Extract box with map and model: 23.930 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.380 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.003 0.045 9744 Z= 0.200 Angle : 0.510 5.699 13238 Z= 0.290 Chirality : 0.038 0.229 1603 Planarity : 0.003 0.033 1597 Dihedral : 13.987 81.514 3444 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.29 % Allowed : 3.05 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.97 (0.25), residues: 1220 helix: 2.44 (0.17), residues: 954 sheet: None (None), residues: 0 loop : 0.27 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 200 HIS 0.002 0.001 HIS B 100 PHE 0.014 0.001 PHE B 98 TYR 0.010 0.001 TYR A 3 ARG 0.002 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7850 (mtp) cc_final: 0.7553 (mtm) REVERT: A 178 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7069 (mmtt) REVERT: A 198 LEU cc_start: 0.8513 (tp) cc_final: 0.8178 (mp) REVERT: A 264 ILE cc_start: 0.8538 (mt) cc_final: 0.8323 (tp) REVERT: A 508 MET cc_start: 0.8623 (mmt) cc_final: 0.8415 (mmm) REVERT: A 566 MET cc_start: 0.8181 (mmm) cc_final: 0.7977 (mmt) REVERT: B 10 TRP cc_start: 0.8262 (m100) cc_final: 0.7987 (m100) REVERT: B 564 MET cc_start: 0.8459 (tpp) cc_final: 0.7890 (tpp) outliers start: 3 outliers final: 0 residues processed: 185 average time/residue: 0.1637 time to fit residues: 45.8752 Evaluate side-chains 114 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 0.0970 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 184 ASN A 228 ASN B 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9744 Z= 0.183 Angle : 0.529 10.629 13238 Z= 0.265 Chirality : 0.039 0.201 1603 Planarity : 0.004 0.030 1597 Dihedral : 5.893 64.295 1340 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.87 % Allowed : 9.23 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.25), residues: 1220 helix: 2.27 (0.17), residues: 961 sheet: None (None), residues: 0 loop : 0.15 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 10 HIS 0.003 0.001 HIS A 285 PHE 0.020 0.001 PHE A 158 TYR 0.015 0.001 TYR A 349 ARG 0.002 0.000 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.058 Fit side-chains REVERT: A 75 MET cc_start: 0.7873 (mtp) cc_final: 0.7651 (mtm) REVERT: A 508 MET cc_start: 0.8635 (mmt) cc_final: 0.8415 (mmm) REVERT: B 204 MET cc_start: 0.8590 (tpp) cc_final: 0.8373 (tpt) REVERT: B 304 ASP cc_start: 0.7921 (t0) cc_final: 0.7666 (t0) REVERT: B 376 MET cc_start: 0.7179 (mmt) cc_final: 0.6945 (mmt) REVERT: B 378 MET cc_start: 0.8713 (tpp) cc_final: 0.8358 (tpp) REVERT: B 481 MET cc_start: 0.9119 (tmm) cc_final: 0.8890 (tmm) REVERT: B 564 MET cc_start: 0.8416 (tpp) cc_final: 0.7938 (tpp) outliers start: 19 outliers final: 10 residues processed: 128 average time/residue: 0.1691 time to fit residues: 33.7410 Evaluate side-chains 118 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 543 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 0.0050 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9744 Z= 0.191 Angle : 0.524 8.546 13238 Z= 0.261 Chirality : 0.038 0.134 1603 Planarity : 0.004 0.034 1597 Dihedral : 5.825 65.367 1336 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 10.81 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.49 (0.25), residues: 1220 helix: 2.11 (0.17), residues: 961 sheet: None (None), residues: 0 loop : -0.07 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 227 HIS 0.002 0.001 HIS B 65 PHE 0.020 0.001 PHE B 20 TYR 0.013 0.001 TYR B 437 ARG 0.003 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.079 Fit side-chains REVERT: A 75 MET cc_start: 0.8048 (mtp) cc_final: 0.7824 (mtm) REVERT: A 508 MET cc_start: 0.8669 (mmt) cc_final: 0.8445 (mmm) REVERT: B 10 TRP cc_start: 0.8484 (m100) cc_final: 0.8003 (m100) REVERT: B 378 MET cc_start: 0.8830 (tpp) cc_final: 0.8511 (tpp) REVERT: B 564 MET cc_start: 0.8426 (tpp) cc_final: 0.7975 (tpp) outliers start: 20 outliers final: 15 residues processed: 117 average time/residue: 0.1762 time to fit residues: 32.3067 Evaluate side-chains 112 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9744 Z= 0.284 Angle : 0.571 10.614 13238 Z= 0.288 Chirality : 0.040 0.149 1603 Planarity : 0.004 0.036 1597 Dihedral : 5.537 62.460 1336 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.06 % Allowed : 12.97 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.19 (0.25), residues: 1220 helix: 1.94 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 408 HIS 0.005 0.001 HIS B 65 PHE 0.021 0.001 PHE B 167 TYR 0.015 0.001 TYR B 221 ARG 0.002 0.000 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.137 Fit side-chains REVERT: A 75 MET cc_start: 0.8270 (mtp) cc_final: 0.7908 (mtm) REVERT: A 508 MET cc_start: 0.8709 (mmt) cc_final: 0.8463 (mmm) REVERT: B 10 TRP cc_start: 0.8503 (m100) cc_final: 0.8067 (m100) REVERT: B 185 TYR cc_start: 0.6346 (OUTLIER) cc_final: 0.5627 (m-10) REVERT: B 564 MET cc_start: 0.8396 (tpp) cc_final: 0.7932 (tpp) outliers start: 21 outliers final: 14 residues processed: 115 average time/residue: 0.1659 time to fit residues: 29.9407 Evaluate side-chains 109 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9744 Z= 0.255 Angle : 0.551 8.273 13238 Z= 0.274 Chirality : 0.039 0.163 1603 Planarity : 0.004 0.035 1597 Dihedral : 5.410 60.289 1336 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.87 % Allowed : 14.83 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.11 (0.25), residues: 1220 helix: 1.87 (0.17), residues: 953 sheet: None (None), residues: 0 loop : -0.25 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 408 HIS 0.003 0.001 HIS B 100 PHE 0.018 0.001 PHE B 167 TYR 0.012 0.001 TYR B 380 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.084 Fit side-chains REVERT: A 75 MET cc_start: 0.8275 (mtp) cc_final: 0.7890 (mtm) REVERT: A 508 MET cc_start: 0.8730 (mmt) cc_final: 0.8464 (mmm) REVERT: B 10 TRP cc_start: 0.8477 (m100) cc_final: 0.8083 (m100) REVERT: B 185 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5768 (m-10) REVERT: B 378 MET cc_start: 0.8691 (tpp) cc_final: 0.8264 (tpp) REVERT: B 481 MET cc_start: 0.9211 (tmm) cc_final: 0.8950 (tmm) REVERT: B 564 MET cc_start: 0.8389 (tpp) cc_final: 0.7928 (tpp) outliers start: 19 outliers final: 15 residues processed: 112 average time/residue: 0.1697 time to fit residues: 29.5887 Evaluate side-chains 108 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9744 Z= 0.214 Angle : 0.542 10.582 13238 Z= 0.266 Chirality : 0.039 0.172 1603 Planarity : 0.004 0.039 1597 Dihedral : 5.287 59.489 1336 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.96 % Allowed : 15.13 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.20 (0.25), residues: 1220 helix: 1.91 (0.17), residues: 952 sheet: None (None), residues: 0 loop : -0.10 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 408 HIS 0.003 0.001 HIS B 100 PHE 0.019 0.001 PHE B 167 TYR 0.011 0.001 TYR B 380 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 1.060 Fit side-chains REVERT: A 75 MET cc_start: 0.8282 (mtp) cc_final: 0.7895 (mtm) REVERT: A 508 MET cc_start: 0.8737 (mmt) cc_final: 0.8467 (mmm) REVERT: B 10 TRP cc_start: 0.8375 (m100) cc_final: 0.8042 (m100) REVERT: B 185 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.5743 (m-80) REVERT: B 378 MET cc_start: 0.8775 (tpp) cc_final: 0.8444 (tpp) REVERT: B 481 MET cc_start: 0.9198 (tmm) cc_final: 0.8914 (tmm) REVERT: B 564 MET cc_start: 0.8386 (tpp) cc_final: 0.8102 (tpp) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.1647 time to fit residues: 28.1784 Evaluate side-chains 105 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9744 Z= 0.159 Angle : 0.521 9.868 13238 Z= 0.252 Chirality : 0.038 0.187 1603 Planarity : 0.004 0.040 1597 Dihedral : 5.253 58.656 1336 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.57 % Allowed : 15.82 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.36 (0.25), residues: 1220 helix: 2.01 (0.17), residues: 950 sheet: None (None), residues: 0 loop : 0.04 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 408 HIS 0.002 0.001 HIS B 100 PHE 0.021 0.001 PHE B 167 TYR 0.008 0.001 TYR B 380 ARG 0.002 0.000 ARG A 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.058 Fit side-chains REVERT: A 75 MET cc_start: 0.8230 (mtp) cc_final: 0.7866 (mtm) REVERT: A 508 MET cc_start: 0.8726 (mmt) cc_final: 0.8467 (mmm) REVERT: B 10 TRP cc_start: 0.8278 (m100) cc_final: 0.8012 (m100) REVERT: B 185 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.5560 (m-80) REVERT: B 378 MET cc_start: 0.8797 (tpp) cc_final: 0.8438 (tpp) REVERT: B 481 MET cc_start: 0.9199 (tmm) cc_final: 0.8939 (tmm) REVERT: B 564 MET cc_start: 0.8393 (tpp) cc_final: 0.8070 (tpp) outliers start: 16 outliers final: 13 residues processed: 111 average time/residue: 0.1701 time to fit residues: 29.5786 Evaluate side-chains 105 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9744 Z= 0.170 Angle : 0.532 8.553 13238 Z= 0.258 Chirality : 0.038 0.210 1603 Planarity : 0.004 0.039 1597 Dihedral : 5.210 57.733 1336 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.77 % Allowed : 15.91 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.34 (0.25), residues: 1220 helix: 2.00 (0.17), residues: 953 sheet: None (None), residues: 0 loop : -0.03 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 408 HIS 0.002 0.001 HIS B 100 PHE 0.024 0.001 PHE B 167 TYR 0.009 0.001 TYR B 380 ARG 0.001 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 1.010 Fit side-chains REVERT: A 75 MET cc_start: 0.8202 (mtp) cc_final: 0.7859 (mtm) REVERT: A 508 MET cc_start: 0.8736 (mmt) cc_final: 0.8472 (mmm) REVERT: B 10 TRP cc_start: 0.8210 (m100) cc_final: 0.7993 (m100) REVERT: B 185 TYR cc_start: 0.6439 (OUTLIER) cc_final: 0.5584 (m-80) REVERT: B 378 MET cc_start: 0.8831 (tpp) cc_final: 0.8504 (tpp) REVERT: B 481 MET cc_start: 0.9191 (tmm) cc_final: 0.8939 (tmm) REVERT: B 564 MET cc_start: 0.8403 (tpp) cc_final: 0.8084 (tpp) outliers start: 18 outliers final: 14 residues processed: 107 average time/residue: 0.1665 time to fit residues: 28.2134 Evaluate side-chains 108 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- 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: 0.8182 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9744 Z= 0.164 Angle : 0.528 8.393 13238 Z= 0.256 Chirality : 0.038 0.183 1603 Planarity : 0.004 0.039 1597 Dihedral : 5.129 56.864 1336 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.57 % Allowed : 16.31 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.29 (0.25), residues: 1220 helix: 1.96 (0.17), residues: 955 sheet: None (None), residues: 0 loop : -0.02 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 408 HIS 0.004 0.001 HIS A 100 PHE 0.024 0.001 PHE B 167 TYR 0.008 0.001 TYR B 380 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.091 Fit side-chains REVERT: A 75 MET cc_start: 0.8179 (mtp) cc_final: 0.7844 (mtm) REVERT: A 508 MET cc_start: 0.8730 (mmt) cc_final: 0.8473 (mmm) REVERT: B 98 PHE cc_start: 0.8961 (t80) cc_final: 0.8427 (t80) REVERT: B 185 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.5578 (m-80) REVERT: B 204 MET cc_start: 0.8811 (mmm) cc_final: 0.8525 (mmm) REVERT: B 378 MET cc_start: 0.8860 (tpp) cc_final: 0.8509 (tpp) REVERT: B 481 MET cc_start: 0.9195 (tmm) cc_final: 0.8942 (tmm) REVERT: B 564 MET cc_start: 0.8394 (tpp) cc_final: 0.8088 (tpp) outliers start: 16 outliers final: 14 residues processed: 107 average time/residue: 0.1629 time to fit residues: 27.6581 Evaluate side-chains 106 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.8202 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9744 Z= 0.204 Angle : 0.553 8.933 13238 Z= 0.271 Chirality : 0.039 0.223 1603 Planarity : 0.004 0.037 1597 Dihedral : 5.098 56.040 1336 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.77 % Allowed : 16.40 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.20 (0.25), residues: 1220 helix: 1.91 (0.17), residues: 953 sheet: None (None), residues: 0 loop : -0.09 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 10 HIS 0.002 0.001 HIS B 100 PHE 0.028 0.001 PHE B 167 TYR 0.009 0.001 TYR B 380 ARG 0.001 0.000 ARG B 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.094 Fit side-chains REVERT: A 75 MET cc_start: 0.8211 (mtp) cc_final: 0.7871 (mtm) REVERT: A 508 MET cc_start: 0.8748 (mmt) cc_final: 0.8482 (mmm) REVERT: B 98 PHE cc_start: 0.8968 (t80) cc_final: 0.8423 (t80) REVERT: B 185 TYR cc_start: 0.6499 (OUTLIER) cc_final: 0.5683 (m-80) REVERT: B 378 MET cc_start: 0.8866 (tpp) cc_final: 0.8574 (tpp) REVERT: B 481 MET cc_start: 0.9201 (tmm) cc_final: 0.8938 (tmm) REVERT: B 564 MET cc_start: 0.8413 (tpp) cc_final: 0.8096 (tpp) outliers start: 18 outliers final: 15 residues processed: 105 average time/residue: 0.1668 time to fit residues: 27.8628 Evaluate side-chains 107 residues out of total 1018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 594 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.0030 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.095122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072649 restraints weight = 24033.532| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.18 r_work: 0.3026 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9744 Z= 0.154 Angle : 0.544 10.629 13238 Z= 0.266 Chirality : 0.038 0.192 1603 Planarity : 0.004 0.039 1597 Dihedral : 5.004 56.238 1336 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.38 % Allowed : 16.60 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.30 (0.25), residues: 1220 helix: 1.96 (0.17), residues: 954 sheet: None (None), residues: 0 loop : -0.01 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 10 HIS 0.002 0.001 HIS B 100 PHE 0.028 0.001 PHE B 167 TYR 0.008 0.001 TYR B 380 ARG 0.001 0.000 ARG A 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.20 seconds wall clock time: 41 minutes 12.76 seconds (2472.76 seconds total)