Starting phenix.real_space_refine on Sun Apr 7 01:20:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/04_2024/6qvc_4647.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/04_2024/6qvc_4647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/04_2024/6qvc_4647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/04_2024/6qvc_4647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/04_2024/6qvc_4647.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/04_2024/6qvc_4647.pdb" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6132 2.51 5 N 1484 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 858": "NH1" <-> "NH2" 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: 9272 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4636 Classifications: {'peptide': 599} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 569} Chain breaks: 3 Chain: "A" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4636 Classifications: {'peptide': 599} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 569} Chain breaks: 3 Time building chain proxies: 5.20, per 1000 atoms: 0.56 Number of scatterers: 9272 At special positions: 0 Unit cell: (105.93, 103.79, 109.14, 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 70 16.00 O 1586 8.00 N 1484 7.00 C 6132 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: 3.54 Conformation dependent library (CDL) restraints added in 1.8 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2216 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 66.4% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'B' and resid 116 through 153 Processing helix chain 'B' and resid 158 through 181 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.413A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.627A pdb=" N PHE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.611A pdb=" N PHE B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.549A pdb=" N ARG B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 377 removed outlier: 4.151A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 391 through 403 removed outlier: 4.691A pdb=" N GLY B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.516A pdb=" N ILE B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 477 removed outlier: 3.530A pdb=" N ILE B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE B 472 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 538 removed outlier: 4.539A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.948A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 586 Processing helix chain 'B' and resid 621 through 632 Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 833 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'A' and resid 116 through 153 Processing helix chain 'A' and resid 158 through 181 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 removed outlier: 4.413A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.626A pdb=" N PHE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.610A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.550A pdb=" N ARG A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 377 removed outlier: 4.151A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 403 removed outlier: 4.691A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.516A pdb=" N ILE A 450 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.530A pdb=" N ILE A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 472 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 4.538A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.949A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 621 through 632 Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 862 through 871 Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'B' and resid 616 through 617 removed outlier: 6.096A pdb=" N VAL B 616 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 822 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853 removed outlier: 6.582A pdb=" N ALA B 849 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 860 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 851 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 617 removed outlier: 6.096A pdb=" N VAL A 616 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 822 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 removed outlier: 6.581A pdb=" N ALA A 849 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 860 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1710 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: 2.78 Time building geometry restraints manager: 3.86 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: 2748 1.34 - 1.46: 2200 1.46 - 1.58: 4440 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 9504 Sorted by residual: bond pdb=" CG1 ILE B 527 " pdb=" CD1 ILE B 527 " ideal model delta sigma weight residual 1.513 1.389 0.124 3.90e-02 6.57e+02 1.02e+01 bond pdb=" CG1 ILE A 527 " pdb=" CD1 ILE A 527 " ideal model delta sigma weight residual 1.513 1.389 0.124 3.90e-02 6.57e+02 1.01e+01 bond pdb=" CB ILE A 354 " pdb=" CG2 ILE A 354 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CB ILE B 354 " pdb=" CG2 ILE B 354 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.63e+00 bond pdb=" C PHE A 343 " pdb=" N ASP A 344 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.40e-02 5.10e+03 5.68e+00 ... (remaining 9499 not shown) Histogram of bond angle deviations from ideal: 94.42 - 102.94: 90 102.94 - 111.46: 4021 111.46 - 119.99: 4800 119.99 - 128.51: 3899 128.51 - 137.03: 104 Bond angle restraints: 12914 Sorted by residual: angle pdb=" C PHE A 343 " pdb=" N ASP A 344 " pdb=" CA ASP A 344 " ideal model delta sigma weight residual 121.70 132.56 -10.86 1.80e+00 3.09e-01 3.64e+01 angle pdb=" C PHE B 343 " pdb=" N ASP B 344 " pdb=" CA ASP B 344 " ideal model delta sigma weight residual 121.70 132.48 -10.78 1.80e+00 3.09e-01 3.59e+01 angle pdb=" CA LEU A 171 " pdb=" CB LEU A 171 " pdb=" CG LEU A 171 " ideal model delta sigma weight residual 116.30 137.03 -20.73 3.50e+00 8.16e-02 3.51e+01 angle pdb=" CA LEU B 171 " pdb=" CB LEU B 171 " pdb=" CG LEU B 171 " ideal model delta sigma weight residual 116.30 136.99 -20.69 3.50e+00 8.16e-02 3.49e+01 angle pdb=" C THR B 621 " pdb=" N TYR B 622 " pdb=" CA TYR B 622 " ideal model delta sigma weight residual 120.82 128.30 -7.48 1.50e+00 4.44e-01 2.49e+01 ... (remaining 12909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.08: 4989 14.08 - 28.16: 433 28.16 - 42.24: 108 42.24 - 56.32: 20 56.32 - 70.40: 6 Dihedral angle restraints: 5556 sinusoidal: 2114 harmonic: 3442 Sorted by residual: dihedral pdb=" CA ALA A 326 " pdb=" C ALA A 326 " pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta harmonic sigma weight residual 180.00 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA ALA B 326 " pdb=" C ALA B 326 " pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta harmonic sigma weight residual 180.00 -135.14 -44.86 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA ILE B 290 " pdb=" C ILE B 290 " pdb=" N GLU B 291 " pdb=" CA GLU B 291 " ideal model delta harmonic sigma weight residual -180.00 -145.15 -34.85 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 5553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1322 0.112 - 0.225: 171 0.225 - 0.337: 31 0.337 - 0.450: 0 0.450 - 0.562: 2 Chirality restraints: 1526 Sorted by residual: chirality pdb=" CB VAL B 321 " pdb=" CA VAL B 321 " pdb=" CG1 VAL B 321 " pdb=" CG2 VAL B 321 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CB VAL A 321 " pdb=" CA VAL A 321 " pdb=" CG1 VAL A 321 " pdb=" CG2 VAL A 321 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" CB ILE B 329 " pdb=" CA ILE B 329 " pdb=" CG1 ILE B 329 " pdb=" CG2 ILE B 329 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1523 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 469 " 0.035 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 469 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 469 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 469 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 469 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 469 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 469 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 469 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 469 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 469 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 469 " -0.035 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP A 469 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 469 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 469 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 469 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 469 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 469 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 469 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 469 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 469 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 327 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C VAL A 327 " -0.056 2.00e-02 2.50e+03 pdb=" O VAL A 327 " 0.021 2.00e-02 2.50e+03 pdb=" N THR A 328 " 0.019 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1622 2.77 - 3.30: 9375 3.30 - 3.83: 15743 3.83 - 4.37: 17403 4.37 - 4.90: 28449 Nonbonded interactions: 72592 Sorted by model distance: nonbonded pdb=" O ILE A 472 " pdb=" OG1 THR A 476 " model vdw 2.232 2.440 nonbonded pdb=" O ILE B 472 " pdb=" OG1 THR B 476 " model vdw 2.232 2.440 nonbonded pdb=" O ILE B 401 " pdb=" OG1 THR B 405 " model vdw 2.237 2.440 nonbonded pdb=" O ILE A 401 " pdb=" OG1 THR A 405 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR B 632 " pdb=" NH1 ARG B 654 " model vdw 2.249 2.520 ... (remaining 72587 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.530 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.800 Find NCS groups from input model: 0.500 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 9504 Z= 0.520 Angle : 1.474 20.735 12914 Z= 0.771 Chirality : 0.080 0.562 1526 Planarity : 0.010 0.059 1580 Dihedral : 11.978 70.398 3340 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.38 % Favored : 91.12 % Rotamer: Outliers : 2.19 % Allowed : 8.95 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: -3.90 (0.20), residues: 1182 helix: -2.23 (0.15), residues: 758 sheet: -0.42 (0.90), residues: 20 loop : -3.15 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP A 469 HIS 0.008 0.002 HIS A 835 PHE 0.037 0.004 PHE A 547 TYR 0.031 0.003 TYR B 589 ARG 0.008 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 225 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.9707 (tt) cc_final: 0.9435 (pp) REVERT: B 128 MET cc_start: 0.9329 (tpp) cc_final: 0.8931 (tpp) REVERT: B 194 MET cc_start: 0.8984 (ppp) cc_final: 0.8701 (ppp) REVERT: B 277 CYS cc_start: 0.8164 (t) cc_final: 0.7599 (t) REVERT: B 301 ASN cc_start: 0.8804 (m-40) cc_final: 0.8440 (m-40) REVERT: B 302 TYR cc_start: 0.9326 (t80) cc_final: 0.9018 (t80) REVERT: B 307 PHE cc_start: 0.8795 (t80) cc_final: 0.8593 (t80) REVERT: B 323 ASN cc_start: 0.8838 (m-40) cc_final: 0.8169 (m-40) REVERT: B 385 PHE cc_start: 0.8736 (t80) cc_final: 0.8525 (m-80) REVERT: B 432 THR cc_start: 0.9306 (m) cc_final: 0.9076 (p) REVERT: B 472 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8956 (mt) REVERT: B 609 MET cc_start: 0.7621 (ptp) cc_final: 0.7252 (pmm) REVERT: B 614 LYS cc_start: 0.9531 (pmtt) cc_final: 0.9305 (tptp) REVERT: B 865 GLU cc_start: 0.9364 (mp0) cc_final: 0.9076 (mp0) REVERT: B 868 LYS cc_start: 0.9471 (mttt) cc_final: 0.9236 (mttt) REVERT: A 126 LEU cc_start: 0.9734 (tt) cc_final: 0.9443 (pp) REVERT: A 128 MET cc_start: 0.9410 (tpp) cc_final: 0.8982 (tpp) REVERT: A 173 LEU cc_start: 0.8987 (pp) cc_final: 0.8774 (pp) REVERT: A 194 MET cc_start: 0.8837 (ppp) cc_final: 0.8486 (ppp) REVERT: A 250 MET cc_start: 0.9139 (tpt) cc_final: 0.8934 (tpp) REVERT: A 277 CYS cc_start: 0.7868 (t) cc_final: 0.7333 (t) REVERT: A 301 ASN cc_start: 0.8730 (m-40) cc_final: 0.8333 (m-40) REVERT: A 302 TYR cc_start: 0.9336 (t80) cc_final: 0.9006 (t80) REVERT: A 323 ASN cc_start: 0.8910 (m-40) cc_final: 0.8260 (m-40) REVERT: A 432 THR cc_start: 0.9388 (m) cc_final: 0.9105 (p) REVERT: A 466 MET cc_start: 0.8711 (tpt) cc_final: 0.8471 (tpt) REVERT: A 472 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8952 (tt) REVERT: A 865 GLU cc_start: 0.9546 (mp0) cc_final: 0.9319 (mp0) REVERT: A 868 LYS cc_start: 0.9536 (mttt) cc_final: 0.9322 (mttt) outliers start: 22 outliers final: 1 residues processed: 234 average time/residue: 0.2334 time to fit residues: 75.7785 Evaluate side-chains 135 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 472 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.0170 chunk 107 optimal weight: 0.0040 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS B 658 GLN A 451 HIS A 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9504 Z= 0.209 Angle : 0.894 12.835 12914 Z= 0.429 Chirality : 0.046 0.174 1526 Planarity : 0.006 0.049 1580 Dihedral : 6.977 51.901 1268 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.58 % Allowed : 16.10 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.59 (0.24), residues: 1182 helix: -0.18 (0.18), residues: 764 sheet: -0.28 (0.97), residues: 20 loop : -2.81 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 469 HIS 0.009 0.001 HIS B 838 PHE 0.041 0.002 PHE A 547 TYR 0.011 0.001 TYR A 524 ARG 0.003 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9188 (tpp) cc_final: 0.8850 (tpp) REVERT: B 194 MET cc_start: 0.8884 (ppp) cc_final: 0.8581 (ppp) REVERT: B 302 TYR cc_start: 0.9415 (t80) cc_final: 0.8997 (t80) REVERT: B 341 PHE cc_start: 0.7739 (t80) cc_final: 0.7535 (t80) REVERT: B 504 MET cc_start: 0.9111 (tmm) cc_final: 0.8864 (tmm) REVERT: B 826 PHE cc_start: 0.6712 (p90) cc_final: 0.6369 (p90) REVERT: A 128 MET cc_start: 0.9277 (tpp) cc_final: 0.8907 (tpp) REVERT: A 173 LEU cc_start: 0.9035 (pp) cc_final: 0.8833 (pp) REVERT: A 194 MET cc_start: 0.8704 (ppp) cc_final: 0.8364 (ppp) REVERT: A 250 MET cc_start: 0.9116 (tpt) cc_final: 0.8879 (tpp) REVERT: A 302 TYR cc_start: 0.9401 (t80) cc_final: 0.9018 (t80) REVERT: A 466 MET cc_start: 0.8681 (tpt) cc_final: 0.8199 (tpp) REVERT: A 470 MET cc_start: 0.8337 (mmm) cc_final: 0.7409 (mmm) REVERT: A 868 LYS cc_start: 0.9584 (mttt) cc_final: 0.9382 (mttm) outliers start: 36 outliers final: 10 residues processed: 202 average time/residue: 0.1739 time to fit residues: 51.9353 Evaluate side-chains 145 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 ASN ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9504 Z= 0.208 Angle : 0.869 13.150 12914 Z= 0.410 Chirality : 0.046 0.205 1526 Planarity : 0.005 0.055 1580 Dihedral : 5.923 36.477 1264 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.27 % Allowed : 17.89 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.62 (0.25), residues: 1182 helix: 0.76 (0.19), residues: 756 sheet: -0.14 (0.96), residues: 20 loop : -2.76 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 469 HIS 0.006 0.001 HIS B 838 PHE 0.037 0.002 PHE A 547 TYR 0.012 0.001 TYR A 620 ARG 0.003 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: B 128 MET cc_start: 0.9123 (tpp) cc_final: 0.8825 (tpp) REVERT: B 194 MET cc_start: 0.8900 (ppp) cc_final: 0.8582 (ppp) REVERT: B 246 LEU cc_start: 0.9785 (tp) cc_final: 0.9562 (tp) REVERT: B 302 TYR cc_start: 0.9431 (t80) cc_final: 0.8965 (t80) REVERT: B 548 GLU cc_start: 0.8791 (tt0) cc_final: 0.8529 (tt0) REVERT: B 826 PHE cc_start: 0.6842 (p90) cc_final: 0.6590 (p90) REVERT: A 128 MET cc_start: 0.9239 (tpp) cc_final: 0.8935 (tpp) REVERT: A 160 GLN cc_start: 0.9168 (mt0) cc_final: 0.8754 (mp10) REVERT: A 194 MET cc_start: 0.8722 (ppp) cc_final: 0.8342 (ppp) REVERT: A 302 TYR cc_start: 0.9436 (t80) cc_final: 0.8988 (t80) REVERT: A 548 GLU cc_start: 0.8911 (tt0) cc_final: 0.8635 (tt0) REVERT: A 826 PHE cc_start: 0.6675 (p90) cc_final: 0.6283 (p90) outliers start: 43 outliers final: 26 residues processed: 181 average time/residue: 0.1634 time to fit residues: 44.7741 Evaluate side-chains 156 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 615 PHE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 ASN B 323 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9504 Z= 0.313 Angle : 0.876 10.984 12914 Z= 0.427 Chirality : 0.047 0.226 1526 Planarity : 0.005 0.050 1580 Dihedral : 5.810 46.945 1264 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.67 % Allowed : 17.79 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.43 (0.25), residues: 1182 helix: 0.90 (0.18), residues: 770 sheet: -0.31 (0.93), residues: 20 loop : -2.78 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 469 HIS 0.005 0.001 HIS B 838 PHE 0.029 0.002 PHE A 547 TYR 0.010 0.001 TYR A 620 ARG 0.003 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 128 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: B 135 MET cc_start: 0.9538 (ptp) cc_final: 0.9266 (ptp) REVERT: B 194 MET cc_start: 0.8883 (ppp) cc_final: 0.8450 (ppp) REVERT: B 246 LEU cc_start: 0.9792 (tp) cc_final: 0.9565 (tp) REVERT: B 302 TYR cc_start: 0.9493 (t80) cc_final: 0.8923 (t80) REVERT: B 391 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8548 (tp) REVERT: B 826 PHE cc_start: 0.7008 (p90) cc_final: 0.6687 (p90) REVERT: A 194 MET cc_start: 0.8723 (ppp) cc_final: 0.8440 (ppp) REVERT: A 302 TYR cc_start: 0.9468 (t80) cc_final: 0.8909 (t80) REVERT: A 477 MET cc_start: 0.8512 (ptp) cc_final: 0.8132 (ptp) outliers start: 57 outliers final: 33 residues processed: 168 average time/residue: 0.1596 time to fit residues: 41.5528 Evaluate side-chains 144 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 590 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9504 Z= 0.218 Angle : 0.844 11.876 12914 Z= 0.393 Chirality : 0.045 0.212 1526 Planarity : 0.004 0.050 1580 Dihedral : 5.507 44.946 1264 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.17 % Allowed : 19.58 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 (0.25), residues: 1182 helix: 1.32 (0.19), residues: 762 sheet: -0.60 (0.91), residues: 20 loop : -2.72 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 469 HIS 0.006 0.001 HIS B 838 PHE 0.031 0.002 PHE A 547 TYR 0.010 0.001 TYR B 137 ARG 0.002 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 135 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 178 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.9014 (m-80) REVERT: B 194 MET cc_start: 0.8859 (ppp) cc_final: 0.8560 (ppp) REVERT: B 246 LEU cc_start: 0.9764 (tp) cc_final: 0.9552 (tp) REVERT: B 250 MET cc_start: 0.9153 (tpp) cc_final: 0.8933 (tpt) REVERT: B 302 TYR cc_start: 0.9463 (t80) cc_final: 0.8888 (t80) REVERT: B 322 TRP cc_start: 0.7558 (OUTLIER) cc_final: 0.7006 (m100) REVERT: B 373 MET cc_start: 0.9136 (mmm) cc_final: 0.8864 (mtp) REVERT: B 391 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8592 (tp) REVERT: B 826 PHE cc_start: 0.6993 (p90) cc_final: 0.6662 (p90) REVERT: A 128 MET cc_start: 0.9171 (tpp) cc_final: 0.8903 (tpp) REVERT: A 178 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8813 (m-80) REVERT: A 194 MET cc_start: 0.8767 (ppp) cc_final: 0.8462 (ppp) REVERT: A 302 TYR cc_start: 0.9464 (t80) cc_final: 0.8881 (t80) REVERT: A 477 MET cc_start: 0.8348 (ptp) cc_final: 0.7879 (ptp) REVERT: A 826 PHE cc_start: 0.6815 (p90) cc_final: 0.6444 (p90) outliers start: 52 outliers final: 27 residues processed: 172 average time/residue: 0.1571 time to fit residues: 41.4455 Evaluate side-chains 153 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 568 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.0050 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9504 Z= 0.201 Angle : 0.887 13.984 12914 Z= 0.404 Chirality : 0.045 0.220 1526 Planarity : 0.005 0.067 1580 Dihedral : 5.342 45.987 1264 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.57 % Allowed : 21.07 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1182 helix: 1.56 (0.19), residues: 748 sheet: -0.67 (0.93), residues: 20 loop : -2.48 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 164 HIS 0.006 0.001 HIS B 838 PHE 0.031 0.001 PHE A 547 TYR 0.010 0.001 TYR B 524 ARG 0.002 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 135 MET cc_start: 0.9531 (ptp) cc_final: 0.9227 (ptp) REVERT: B 153 MET cc_start: 0.8893 (ppp) cc_final: 0.8471 (ppp) REVERT: B 194 MET cc_start: 0.8864 (ppp) cc_final: 0.8597 (ppp) REVERT: B 246 LEU cc_start: 0.9765 (tp) cc_final: 0.9552 (tp) REVERT: B 250 MET cc_start: 0.9118 (tpp) cc_final: 0.8885 (tpt) REVERT: B 373 MET cc_start: 0.9112 (mmm) cc_final: 0.8894 (mtm) REVERT: B 504 MET cc_start: 0.9074 (tmm) cc_final: 0.8818 (ppp) REVERT: B 826 PHE cc_start: 0.6779 (p90) cc_final: 0.6422 (p90) REVERT: A 128 MET cc_start: 0.9148 (tpp) cc_final: 0.8812 (tpp) REVERT: A 178 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8864 (m-80) REVERT: A 194 MET cc_start: 0.8825 (ppp) cc_final: 0.8525 (ppp) REVERT: A 302 TYR cc_start: 0.9491 (t80) cc_final: 0.8834 (t80) REVERT: A 477 MET cc_start: 0.8397 (ptp) cc_final: 0.8010 (ptp) REVERT: A 502 MET cc_start: 0.9338 (tpp) cc_final: 0.9125 (tpp) outliers start: 46 outliers final: 31 residues processed: 169 average time/residue: 0.1567 time to fit residues: 40.8512 Evaluate side-chains 156 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 10.0000 chunk 12 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9504 Z= 0.202 Angle : 0.899 12.660 12914 Z= 0.405 Chirality : 0.046 0.219 1526 Planarity : 0.005 0.061 1580 Dihedral : 5.241 46.095 1264 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.17 % Allowed : 22.37 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.38 (0.25), residues: 1182 helix: 1.65 (0.19), residues: 754 sheet: -0.56 (0.96), residues: 20 loop : -2.55 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.006 0.000 HIS B 838 PHE 0.034 0.001 PHE A 547 TYR 0.022 0.001 TYR B 302 ARG 0.001 0.000 ARG B 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.8877 (ppp) cc_final: 0.8481 (ppp) REVERT: B 194 MET cc_start: 0.8857 (ppp) cc_final: 0.8631 (ppp) REVERT: B 246 LEU cc_start: 0.9764 (tp) cc_final: 0.9552 (tp) REVERT: A 178 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: A 194 MET cc_start: 0.8784 (ppp) cc_final: 0.8495 (ppp) REVERT: A 302 TYR cc_start: 0.9468 (t80) cc_final: 0.8859 (t80) REVERT: A 477 MET cc_start: 0.8453 (ptp) cc_final: 0.8188 (ptp) REVERT: A 502 MET cc_start: 0.9345 (tpp) cc_final: 0.9135 (tpp) REVERT: A 826 PHE cc_start: 0.6684 (p90) cc_final: 0.6342 (p90) outliers start: 42 outliers final: 31 residues processed: 156 average time/residue: 0.1672 time to fit residues: 39.8720 Evaluate side-chains 155 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 322 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 568 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 323 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9504 Z= 0.223 Angle : 0.919 12.928 12914 Z= 0.415 Chirality : 0.046 0.288 1526 Planarity : 0.005 0.057 1580 Dihedral : 5.215 46.816 1264 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.98 % Allowed : 23.16 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.38 (0.25), residues: 1182 helix: 1.62 (0.19), residues: 756 sheet: -0.42 (0.98), residues: 20 loop : -2.51 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 469 HIS 0.020 0.001 HIS B 369 PHE 0.032 0.002 PHE A 547 TYR 0.020 0.001 TYR B 302 ARG 0.002 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.8909 (tpp) cc_final: 0.8672 (tpp) REVERT: B 153 MET cc_start: 0.8915 (ppp) cc_final: 0.8578 (ppp) REVERT: B 194 MET cc_start: 0.8916 (ppp) cc_final: 0.8617 (ppp) REVERT: B 826 PHE cc_start: 0.6729 (p90) cc_final: 0.6435 (p90) REVERT: A 178 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8981 (m-80) REVERT: A 194 MET cc_start: 0.8813 (ppp) cc_final: 0.8520 (ppp) REVERT: A 477 MET cc_start: 0.8540 (ptp) cc_final: 0.8312 (ptp) REVERT: A 502 MET cc_start: 0.9349 (tpp) cc_final: 0.9147 (tpp) REVERT: A 826 PHE cc_start: 0.6747 (p90) cc_final: 0.6369 (p90) outliers start: 40 outliers final: 34 residues processed: 158 average time/residue: 0.1585 time to fit residues: 38.3619 Evaluate side-chains 159 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 614 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 46 optimal weight: 0.0070 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9504 Z= 0.201 Angle : 0.936 13.329 12914 Z= 0.418 Chirality : 0.047 0.332 1526 Planarity : 0.004 0.056 1580 Dihedral : 5.138 46.504 1264 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.08 % Allowed : 23.36 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.48 (0.26), residues: 1182 helix: 1.70 (0.19), residues: 756 sheet: -0.34 (1.01), residues: 20 loop : -2.46 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 469 HIS 0.015 0.001 HIS B 369 PHE 0.033 0.001 PHE A 547 TYR 0.020 0.001 TYR B 302 ARG 0.004 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 136 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.8913 (ppp) cc_final: 0.8611 (ppp) REVERT: B 194 MET cc_start: 0.8875 (ppp) cc_final: 0.8632 (ppp) REVERT: B 504 MET cc_start: 0.9205 (ppp) cc_final: 0.8884 (ppp) REVERT: B 826 PHE cc_start: 0.6627 (p90) cc_final: 0.6338 (p90) REVERT: A 194 MET cc_start: 0.8798 (ppp) cc_final: 0.8508 (ppp) REVERT: A 332 LEU cc_start: 0.9034 (mt) cc_final: 0.8786 (tp) REVERT: A 373 MET cc_start: 0.9046 (mmm) cc_final: 0.8732 (mtp) REVERT: A 477 MET cc_start: 0.8505 (ptp) cc_final: 0.8275 (ptp) REVERT: A 502 MET cc_start: 0.9342 (tpp) cc_final: 0.9141 (tpp) REVERT: A 826 PHE cc_start: 0.6844 (p90) cc_final: 0.6455 (p90) outliers start: 41 outliers final: 32 residues processed: 159 average time/residue: 0.1646 time to fit residues: 39.9531 Evaluate side-chains 161 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 614 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 93 optimal weight: 0.3980 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 323 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9504 Z= 0.208 Angle : 0.949 14.182 12914 Z= 0.424 Chirality : 0.047 0.320 1526 Planarity : 0.004 0.055 1580 Dihedral : 5.119 46.435 1264 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.78 % Allowed : 23.66 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.47 (0.26), residues: 1182 helix: 1.66 (0.19), residues: 756 sheet: -0.26 (1.02), residues: 20 loop : -2.40 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 469 HIS 0.009 0.001 HIS B 369 PHE 0.032 0.001 PHE B 547 TYR 0.012 0.001 TYR B 302 ARG 0.002 0.000 ARG A 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.8929 (ppp) cc_final: 0.8697 (ppp) REVERT: B 194 MET cc_start: 0.8894 (ppp) cc_final: 0.8641 (ppp) REVERT: B 504 MET cc_start: 0.9245 (ppp) cc_final: 0.8915 (ppp) REVERT: B 826 PHE cc_start: 0.6634 (p90) cc_final: 0.6335 (p90) REVERT: A 128 MET cc_start: 0.8987 (tpp) cc_final: 0.8764 (tpp) REVERT: A 194 MET cc_start: 0.8816 (ppp) cc_final: 0.8543 (ppp) REVERT: A 373 MET cc_start: 0.9051 (mmm) cc_final: 0.8742 (mtp) REVERT: A 477 MET cc_start: 0.8490 (ptp) cc_final: 0.8235 (ptp) REVERT: A 826 PHE cc_start: 0.6846 (p90) cc_final: 0.6473 (p90) outliers start: 38 outliers final: 33 residues processed: 160 average time/residue: 0.1552 time to fit residues: 37.8202 Evaluate side-chains 161 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 847 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 614 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0670 chunk 86 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 0.0010 overall best weight: 0.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 ASN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056703 restraints weight = 40439.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.058410 restraints weight = 24134.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.059601 restraints weight = 16603.384| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9504 Z= 0.202 Angle : 0.964 14.025 12914 Z= 0.429 Chirality : 0.048 0.323 1526 Planarity : 0.004 0.055 1580 Dihedral : 5.069 46.001 1264 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.88 % Allowed : 24.35 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.48 (0.25), residues: 1182 helix: 1.65 (0.19), residues: 756 sheet: -0.12 (1.03), residues: 20 loop : -2.37 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 164 HIS 0.010 0.001 HIS B 369 PHE 0.031 0.001 PHE B 547 TYR 0.011 0.001 TYR B 302 ARG 0.003 0.000 ARG B 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.31 seconds wall clock time: 36 minutes 15.85 seconds (2175.85 seconds total)