Starting phenix.real_space_refine on Mon Mar 11 07:04:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/03_2024/6nph_0470_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/03_2024/6nph_0470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/03_2024/6nph_0470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/03_2024/6nph_0470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/03_2024/6nph_0470_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/03_2024/6nph_0470_updated.pdb" } resolution = 2.9 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= 0.013 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 7 5.49 5 S 46 5.16 5 Cl 4 4.86 5 C 5016 2.51 5 N 1119 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ASP 468": "OD1" <-> "OD2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 630": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ASP 468": "OD1" <-> "OD2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 630": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7504 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3567 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain: "B" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3567 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 13, 'TRANS': 458} Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 159 Unusual residues: {' K': 1, ' CL': 2, 'POV': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 211 Unusual residues: {' K': 1, ' CL': 2, 'POV': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 4.65, per 1000 atoms: 0.62 Number of scatterers: 7504 At special positions: 0 Unit cell: (105.5, 77.015, 90.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 46 16.00 P 7 15.00 O 1310 8.00 N 1119 7.00 C 5016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 496 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 507 " distance=2.03 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: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 0 sheets defined 61.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 209 through 221 removed outlier: 4.954A pdb=" N VAL A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 239 through 264 Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.681A pdb=" N ILE A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 319 removed outlier: 3.741A pdb=" N SER A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.580A pdb=" N ILE A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 350 through 374 removed outlier: 4.110A pdb=" N ALA A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 412 through 418 Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 435 through 462 Proline residue: A 440 - end of helix removed outlier: 3.691A pdb=" N LEU A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 Processing helix chain 'A' and resid 529 through 544 removed outlier: 3.901A pdb=" N ILE A 532 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 533 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 536 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 537 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 538 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 540 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 554 Processing helix chain 'A' and resid 562 through 565 removed outlier: 4.496A pdb=" N ILE A 565 " --> pdb=" O GLY A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 565' Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.572A pdb=" N PHE A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 623 Proline residue: A 601 - end of helix Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 657 through 675 removed outlier: 3.646A pdb=" N VAL A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 4.955A pdb=" N VAL B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 239 through 264 Processing helix chain 'B' and resid 274 through 281 removed outlier: 3.681A pdb=" N ILE B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 319 removed outlier: 3.743A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 340 removed outlier: 3.581A pdb=" N ILE B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 Processing helix chain 'B' and resid 350 through 374 removed outlier: 4.110A pdb=" N ALA B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 412 through 418 Proline residue: B 417 - end of helix Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 435 through 462 Proline residue: B 440 - end of helix removed outlier: 3.692A pdb=" N LEU B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 529 through 544 removed outlier: 3.901A pdb=" N ILE B 532 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 533 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 536 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 554 Processing helix chain 'B' and resid 562 through 565 removed outlier: 4.495A pdb=" N ILE B 565 " --> pdb=" O GLY B 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 562 through 565' Processing helix chain 'B' and resid 577 through 591 removed outlier: 3.573A pdb=" N PHE B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 623 Proline residue: B 601 - end of helix Processing helix chain 'B' and resid 638 through 655 Processing helix chain 'B' and resid 657 through 675 removed outlier: 3.645A pdb=" N VAL B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) 364 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1108 1.31 - 1.43: 2113 1.43 - 1.56: 4241 1.56 - 1.69: 124 1.69 - 1.82: 77 Bond restraints: 7663 Sorted by residual: bond pdb=" C31 POV A 702 " pdb=" O31 POV A 702 " ideal model delta sigma weight residual 1.327 1.438 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.436 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C31 POV B 802 " pdb=" O31 POV B 802 " ideal model delta sigma weight residual 1.327 1.432 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C31 POV B 801 " pdb=" O31 POV B 801 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C21 POV A 703 " pdb=" O21 POV A 703 " ideal model delta sigma weight residual 1.330 1.433 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 7658 not shown) Histogram of bond angle deviations from ideal: 79.67 - 90.56: 4 90.56 - 101.46: 24 101.46 - 112.36: 3978 112.36 - 123.26: 6105 123.26 - 134.16: 240 Bond angle restraints: 10351 Sorted by residual: angle pdb=" C12 POV A 703 " pdb=" N POV A 703 " pdb=" C15 POV A 703 " ideal model delta sigma weight residual 112.10 80.99 31.11 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C13 POV A 703 " pdb=" N POV A 703 " pdb=" C14 POV A 703 " ideal model delta sigma weight residual 108.80 79.67 29.13 3.00e+00 1.11e-01 9.43e+01 angle pdb=" C13 POV A 703 " pdb=" N POV A 703 " pdb=" C15 POV A 703 " ideal model delta sigma weight residual 109.35 80.29 29.06 3.00e+00 1.11e-01 9.38e+01 angle pdb=" C12 POV A 703 " pdb=" N POV A 703 " pdb=" C14 POV A 703 " ideal model delta sigma weight residual 107.13 80.42 26.71 3.00e+00 1.11e-01 7.93e+01 angle pdb=" C14 POV A 703 " pdb=" N POV A 703 " pdb=" C15 POV A 703 " ideal model delta sigma weight residual 108.02 132.52 -24.50 3.00e+00 1.11e-01 6.67e+01 ... (remaining 10346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.94: 4223 28.94 - 57.87: 210 57.87 - 86.81: 34 86.81 - 115.75: 5 115.75 - 144.68: 5 Dihedral angle restraints: 4477 sinusoidal: 1791 harmonic: 2686 Sorted by residual: dihedral pdb=" CD ARG A 630 " pdb=" NE ARG A 630 " pdb=" CZ ARG A 630 " pdb=" NH1 ARG A 630 " ideal model delta sinusoidal sigma weight residual 0.00 -41.33 41.33 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CA ALA A 530 " pdb=" C ALA A 530 " pdb=" N GLY A 531 " pdb=" CA GLY A 531 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ALA B 530 " pdb=" C ALA B 530 " pdb=" N GLY B 531 " pdb=" CA GLY B 531 " ideal model delta harmonic sigma weight residual 180.00 155.88 24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 4474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 667 0.043 - 0.085: 360 0.085 - 0.128: 110 0.128 - 0.170: 33 0.170 - 0.213: 7 Chirality restraints: 1177 Sorted by residual: chirality pdb=" CA PHE B 387 " pdb=" N PHE B 387 " pdb=" C PHE B 387 " pdb=" CB PHE B 387 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PHE A 387 " pdb=" N PHE A 387 " pdb=" C PHE A 387 " pdb=" CB PHE A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA SER A 525 " pdb=" N SER A 525 " pdb=" C SER A 525 " pdb=" CB SER A 525 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1174 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 630 " 0.719 9.50e-02 1.11e+02 3.22e-01 6.33e+01 pdb=" NE ARG A 630 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 630 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 630 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 630 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 630 " -0.309 9.50e-02 1.11e+02 1.39e-01 1.18e+01 pdb=" NE ARG B 630 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 630 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 630 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 630 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 416 " 0.047 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO B 417 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 417 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 417 " 0.039 5.00e-02 4.00e+02 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 2665 2.86 - 3.43: 7735 3.43 - 4.00: 13695 4.00 - 4.57: 20364 4.57 - 5.14: 29229 Nonbonded interactions: 73688 Sorted by model distance: nonbonded pdb=" OG SER B 474 " pdb=" O GLY B 490 " model vdw 2.292 2.440 nonbonded pdb=" OG SER A 474 " pdb=" O GLY A 490 " model vdw 2.292 2.440 nonbonded pdb=" O MET A 518 " pdb=" OG SER A 522 " model vdw 2.315 2.440 nonbonded pdb=" O MET B 518 " pdb=" OG SER B 522 " model vdw 2.316 2.440 nonbonded pdb=" OE1 GLN B 406 " pdb=" OG SER B 410 " model vdw 2.322 2.440 ... (remaining 73683 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 206 through 677 or resid 701 through 703 or resid 706)) selection = (chain 'B' and (resid 206 through 677 or resid 801 through 803 or resid 806)) } 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: 0.640 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: 2.720 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.380 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 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 : 0.012 0.111 7663 Z= 0.773 Angle : 1.415 31.111 10351 Z= 0.626 Chirality : 0.058 0.213 1177 Planarity : 0.012 0.322 1243 Dihedral : 18.336 144.683 2763 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.67 % Allowed : 7.73 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.20), residues: 940 helix: -2.32 (0.15), residues: 600 sheet: None (None), residues: 0 loop : -3.64 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 657 HIS 0.003 0.001 HIS A 512 PHE 0.032 0.003 PHE B 387 TYR 0.010 0.002 TYR B 491 ARG 0.004 0.001 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 0.824 Fit side-chains REVERT: A 525 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7876 (p) REVERT: A 568 LYS cc_start: 0.6795 (tttt) cc_final: 0.6162 (tmtm) REVERT: B 211 LYS cc_start: 0.7463 (tttm) cc_final: 0.6281 (mptt) REVERT: B 575 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7341 (pt0) outliers start: 35 outliers final: 6 residues processed: 213 average time/residue: 0.8367 time to fit residues: 191.9176 Evaluate side-chains 121 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 557 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.0000 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 298 ASN A 327 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN A 664 ASN B 298 ASN B 327 GLN B 357 GLN B 512 HIS B 513 ASN B 664 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7663 Z= 0.178 Angle : 0.595 11.799 10351 Z= 0.302 Chirality : 0.041 0.163 1177 Planarity : 0.004 0.053 1243 Dihedral : 16.689 108.471 1309 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 6.40 % Allowed : 14.93 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.26), residues: 940 helix: -0.23 (0.20), residues: 596 sheet: None (None), residues: 0 loop : -3.05 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.014 0.001 PHE A 415 TYR 0.013 0.001 TYR A 371 ARG 0.003 0.001 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 125 time to evaluate : 0.808 Fit side-chains REVERT: A 211 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7916 (mtpt) REVERT: A 525 SER cc_start: 0.7862 (p) cc_final: 0.7656 (p) REVERT: A 568 LYS cc_start: 0.7320 (tttt) cc_final: 0.6775 (tttm) REVERT: A 634 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7779 (ttmt) REVERT: B 304 MET cc_start: 0.8850 (ttp) cc_final: 0.8613 (ttp) REVERT: B 328 THR cc_start: 0.8096 (t) cc_final: 0.7884 (m) REVERT: B 395 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7766 (tm) REVERT: B 479 ILE cc_start: 0.5530 (OUTLIER) cc_final: 0.5189 (mm) REVERT: B 524 PHE cc_start: 0.7794 (t80) cc_final: 0.7120 (t80) outliers start: 48 outliers final: 12 residues processed: 156 average time/residue: 0.8266 time to fit residues: 139.4254 Evaluate side-chains 123 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 GLN B 512 HIS B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7663 Z= 0.211 Angle : 0.546 6.428 10351 Z= 0.285 Chirality : 0.042 0.160 1177 Planarity : 0.003 0.042 1243 Dihedral : 16.286 111.699 1303 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.53 % Allowed : 19.33 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.27), residues: 940 helix: 0.35 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -3.05 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 209 HIS 0.003 0.001 HIS A 512 PHE 0.019 0.001 PHE A 387 TYR 0.011 0.001 TYR B 676 ARG 0.002 0.000 ARG B 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 0.791 Fit side-chains REVERT: A 324 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.5583 (ttt) REVERT: A 350 MET cc_start: 0.7394 (tpp) cc_final: 0.6581 (tpp) REVERT: A 568 LYS cc_start: 0.7849 (tttt) cc_final: 0.7239 (tttm) REVERT: A 634 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: B 315 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6211 (mt-10) REVERT: B 345 ILE cc_start: 0.8457 (mt) cc_final: 0.8167 (mp) REVERT: B 373 ILE cc_start: 0.8669 (pt) cc_final: 0.8165 (mt) REVERT: B 479 ILE cc_start: 0.5901 (OUTLIER) cc_final: 0.5532 (mm) REVERT: B 525 SER cc_start: 0.8409 (OUTLIER) cc_final: 0.8079 (t) outliers start: 34 outliers final: 8 residues processed: 135 average time/residue: 0.8835 time to fit residues: 128.5233 Evaluate side-chains 105 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 610 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7663 Z= 0.220 Angle : 0.537 7.397 10351 Z= 0.279 Chirality : 0.042 0.162 1177 Planarity : 0.003 0.036 1243 Dihedral : 15.966 112.316 1303 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.40 % Allowed : 20.40 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.27), residues: 940 helix: 0.65 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -2.91 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 209 HIS 0.003 0.001 HIS B 512 PHE 0.016 0.001 PHE B 415 TYR 0.011 0.001 TYR A 371 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 2.072 Fit side-chains REVERT: A 315 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7005 (tt0) REVERT: A 324 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.5900 (ttt) REVERT: A 361 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8042 (tm) REVERT: A 381 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8370 (t) REVERT: A 568 LYS cc_start: 0.7990 (tttt) cc_final: 0.7443 (tttm) REVERT: B 315 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6370 (mt-10) REVERT: B 345 ILE cc_start: 0.8401 (mt) cc_final: 0.8153 (mp) REVERT: B 373 ILE cc_start: 0.8698 (pt) cc_final: 0.8393 (mt) REVERT: B 437 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7760 (tmt) REVERT: B 479 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5726 (mm) outliers start: 33 outliers final: 10 residues processed: 118 average time/residue: 0.8782 time to fit residues: 111.8801 Evaluate side-chains 99 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 534 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.7558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7663 Z= 0.156 Angle : 0.491 6.350 10351 Z= 0.256 Chirality : 0.040 0.166 1177 Planarity : 0.003 0.033 1243 Dihedral : 15.406 108.117 1303 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.07 % Allowed : 20.93 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.28), residues: 940 helix: 1.05 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.80 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.013 0.001 PHE B 415 TYR 0.011 0.001 TYR B 371 ARG 0.002 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.815 Fit side-chains REVERT: A 315 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: A 324 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.5801 (ttt) REVERT: A 568 LYS cc_start: 0.7976 (tttt) cc_final: 0.7504 (tttm) REVERT: B 315 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6355 (mt-10) REVERT: B 322 LEU cc_start: 0.8081 (mm) cc_final: 0.7875 (mm) REVERT: B 345 ILE cc_start: 0.8408 (mt) cc_final: 0.8173 (mp) REVERT: B 373 ILE cc_start: 0.8676 (pt) cc_final: 0.8373 (mt) outliers start: 23 outliers final: 6 residues processed: 104 average time/residue: 0.9667 time to fit residues: 107.9114 Evaluate side-chains 90 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 610 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 7663 Z= 0.422 Angle : 0.622 5.787 10351 Z= 0.324 Chirality : 0.047 0.156 1177 Planarity : 0.004 0.033 1243 Dihedral : 16.600 120.060 1303 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.07 % Allowed : 19.60 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 940 helix: 0.57 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -3.02 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 209 HIS 0.003 0.002 HIS B 512 PHE 0.023 0.002 PHE A 387 TYR 0.013 0.002 TYR A 491 ARG 0.004 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 80 time to evaluate : 0.854 Fit side-chains REVERT: A 225 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.5641 (mpt) REVERT: A 229 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8669 (mmt-90) REVERT: A 315 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: A 381 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8433 (t) REVERT: A 568 LYS cc_start: 0.8052 (tttt) cc_final: 0.7507 (tttp) REVERT: A 634 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8091 (ttmt) REVERT: B 315 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6620 (mt-10) REVERT: B 325 ILE cc_start: 0.6466 (OUTLIER) cc_final: 0.6246 (mt) REVERT: B 345 ILE cc_start: 0.8503 (mt) cc_final: 0.8245 (mp) REVERT: B 373 ILE cc_start: 0.8724 (pt) cc_final: 0.8427 (mt) REVERT: B 525 SER cc_start: 0.8415 (OUTLIER) cc_final: 0.8111 (t) outliers start: 38 outliers final: 15 residues processed: 108 average time/residue: 0.9147 time to fit residues: 106.3653 Evaluate side-chains 99 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 76 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 610 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.7923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7663 Z= 0.151 Angle : 0.498 6.156 10351 Z= 0.260 Chirality : 0.041 0.154 1177 Planarity : 0.003 0.031 1243 Dihedral : 15.424 109.665 1303 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.13 % Allowed : 20.80 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 940 helix: 1.15 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.72 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 209 HIS 0.002 0.001 HIS A 512 PHE 0.012 0.001 PHE B 415 TYR 0.012 0.001 TYR B 371 ARG 0.002 0.000 ARG B 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 315 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: A 568 LYS cc_start: 0.8026 (tttt) cc_final: 0.7493 (tttm) REVERT: A 634 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8072 (ttmt) REVERT: B 315 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6419 (mt-10) REVERT: B 525 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8361 (p) outliers start: 31 outliers final: 14 residues processed: 111 average time/residue: 0.9937 time to fit residues: 118.3166 Evaluate side-chains 102 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0170 chunk 17 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 0.0000 chunk 84 optimal weight: 0.6980 overall best weight: 0.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.8014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7663 Z= 0.121 Angle : 0.485 7.549 10351 Z= 0.248 Chirality : 0.040 0.197 1177 Planarity : 0.003 0.030 1243 Dihedral : 14.567 101.323 1303 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.80 % Allowed : 22.67 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 940 helix: 1.52 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.65 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 209 HIS 0.001 0.001 HIS B 512 PHE 0.010 0.001 PHE A 387 TYR 0.016 0.001 TYR B 371 ARG 0.003 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 315 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: A 361 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8047 (tm) REVERT: A 525 SER cc_start: 0.8379 (p) cc_final: 0.8125 (p) REVERT: A 634 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8124 (tppt) REVERT: B 315 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6398 (mt-10) REVERT: B 437 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7471 (tmt) REVERT: B 525 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8430 (p) outliers start: 21 outliers final: 8 residues processed: 110 average time/residue: 0.9525 time to fit residues: 112.9152 Evaluate side-chains 100 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 610 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 0.0770 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.8058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7663 Z= 0.164 Angle : 0.500 7.362 10351 Z= 0.258 Chirality : 0.041 0.185 1177 Planarity : 0.003 0.029 1243 Dihedral : 14.601 103.836 1301 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.93 % Allowed : 22.93 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.28), residues: 940 helix: 1.48 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.61 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 209 HIS 0.002 0.001 HIS B 512 PHE 0.013 0.001 PHE A 387 TYR 0.013 0.001 TYR B 371 ARG 0.002 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 315 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: A 361 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8069 (tm) REVERT: A 525 SER cc_start: 0.8493 (p) cc_final: 0.8256 (p) REVERT: A 634 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8135 (tppt) REVERT: B 315 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6411 (mt-10) REVERT: B 525 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8514 (p) outliers start: 22 outliers final: 10 residues processed: 101 average time/residue: 0.9307 time to fit residues: 101.2703 Evaluate side-chains 101 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.8097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7663 Z= 0.250 Angle : 0.548 7.024 10351 Z= 0.281 Chirality : 0.043 0.196 1177 Planarity : 0.003 0.030 1243 Dihedral : 15.140 109.937 1301 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.67 % Allowed : 23.20 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 940 helix: 1.22 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.78 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 209 HIS 0.003 0.002 HIS A 512 PHE 0.017 0.001 PHE A 387 TYR 0.012 0.001 TYR B 371 ARG 0.002 0.000 ARG B 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.851 Fit side-chains REVERT: A 225 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.5930 (mpt) REVERT: A 361 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8195 (tm) REVERT: A 518 MET cc_start: 0.8681 (mmt) cc_final: 0.7965 (mmt) REVERT: A 634 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8126 (ttmt) REVERT: B 525 SER cc_start: 0.8627 (OUTLIER) cc_final: 0.8349 (p) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.9053 time to fit residues: 91.6457 Evaluate side-chains 95 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 507 CYS Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 610 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.089624 restraints weight = 8932.434| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.93 r_work: 0.2804 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.8136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7663 Z= 0.309 Angle : 0.587 9.050 10351 Z= 0.301 Chirality : 0.045 0.211 1177 Planarity : 0.003 0.032 1243 Dihedral : 15.620 114.848 1301 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.67 % Allowed : 23.33 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.28), residues: 940 helix: 0.97 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -2.86 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 209 HIS 0.004 0.002 HIS A 512 PHE 0.019 0.002 PHE A 387 TYR 0.012 0.001 TYR B 371 ARG 0.002 0.000 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2661.64 seconds wall clock time: 48 minutes 12.56 seconds (2892.56 seconds total)