Starting phenix.real_space_refine (version: dev) on Sat Feb 18 06:33:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/02_2023/6nph_0470_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/02_2023/6nph_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_0470/02_2023/6nph_0470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/02_2023/6nph_0470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/02_2023/6nph_0470_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nph_0470/02_2023/6nph_0470_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 4.77, per 1000 atoms: 0.64 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: 2.83 Conformation dependent library (CDL) restraints added in 1.2 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: 0.72 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: 2.04 Time building geometry restraints manager: 3.07 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: 4208 28.94 - 57.87: 190 57.87 - 86.81: 27 86.81 - 115.75: 5 115.75 - 144.68: 5 Dihedral angle restraints: 4435 sinusoidal: 1749 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 4432 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 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. 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: 0.370 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: 2.880 Check model and map are aligned: 0.110 Process input model: 23.450 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 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 : 17.825 144.683 2721 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 % 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 *********************** 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 : 0.761 Fit side-chains outliers start: 35 outliers final: 6 residues processed: 213 average time/residue: 0.8507 time to fit residues: 194.9663 Evaluate side-chains 119 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.2334 time to fit residues: 1.3753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 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: 0.5784 ------------------------------------------------------------------------------- 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: 0.7878 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7663 Z= 0.176 Angle : 0.589 12.845 10351 Z= 0.301 Chirality : 0.042 0.162 1177 Planarity : 0.004 0.051 1243 Dihedral : 15.519 104.435 1257 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer Outliers : 6.00 % 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: -1.84 (0.26), residues: 940 helix: -0.17 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -3.07 (0.28), residues: 352 *********************** 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 178 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 133 time to evaluate : 0.792 Fit side-chains outliers start: 45 outliers final: 14 residues processed: 158 average time/residue: 0.7344 time to fit residues: 126.3554 Evaluate side-chains 120 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.3246 time to fit residues: 2.5709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8244 moved from start: 0.6640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7663 Z= 0.204 Angle : 0.562 6.849 10351 Z= 0.292 Chirality : 0.042 0.164 1177 Planarity : 0.004 0.040 1243 Dihedral : 15.475 109.114 1257 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 4.67 % 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: -1.22 (0.27), residues: 940 helix: 0.36 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.04 (0.29), residues: 340 *********************** 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 148 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 0.712 Fit side-chains outliers start: 35 outliers final: 7 residues processed: 136 average time/residue: 0.8193 time to fit residues: 121.1116 Evaluate side-chains 98 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.0901 time to fit residues: 1.3490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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: 0.8282 moved from start: 0.7266 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= 0.206 Angle : 0.527 7.884 10351 Z= 0.274 Chirality : 0.041 0.171 1177 Planarity : 0.003 0.036 1243 Dihedral : 15.026 109.309 1257 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 4.27 % 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: -0.81 (0.27), residues: 940 helix: 0.75 (0.22), residues: 598 sheet: None (None), residues: 0 loop : -3.01 (0.29), residues: 342 *********************** 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 130 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 0.744 Fit side-chains outliers start: 32 outliers final: 10 residues processed: 120 average time/residue: 0.7841 time to fit residues: 102.4131 Evaluate side-chains 91 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.0804 time to fit residues: 1.4368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 30 optimal weight: 0.0020 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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: 0.8266 moved from start: 0.7478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 7663 Z= 0.149 Angle : 0.495 7.694 10351 Z= 0.257 Chirality : 0.040 0.157 1177 Planarity : 0.003 0.033 1243 Dihedral : 14.396 101.939 1257 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 3.33 % 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: -0.39 (0.28), residues: 940 helix: 1.15 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -2.87 (0.29), residues: 350 *********************** 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 115 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.792 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 107 average time/residue: 0.9348 time to fit residues: 107.5033 Evaluate side-chains 94 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.0710 time to fit residues: 1.3669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 53 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 516 GLN B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.7942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.058 7663 Z= 0.528 Angle : 0.690 7.522 10351 Z= 0.356 Chirality : 0.050 0.210 1177 Planarity : 0.004 0.033 1243 Dihedral : 16.420 120.722 1257 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer Outliers : 4.00 % 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: -1.16 (0.27), residues: 940 helix: 0.41 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -3.11 (0.30), residues: 330 *********************** 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 110 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 0.780 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 103 average time/residue: 0.9649 time to fit residues: 106.9372 Evaluate side-chains 89 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.7619 time to fit residues: 3.5471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8303 moved from start: 0.7985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7663 Z= 0.166 Angle : 0.520 7.252 10351 Z= 0.270 Chirality : 0.041 0.171 1177 Planarity : 0.003 0.030 1243 Dihedral : 14.996 112.723 1257 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 3.47 % 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: 1.03 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.86 (0.31), residues: 338 *********************** 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 114 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.803 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 107 average time/residue: 0.8495 time to fit residues: 98.4380 Evaluate side-chains 96 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.0808 time to fit residues: 1.4115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 512 HIS B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.8020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 7663 Z= 0.168 Angle : 0.523 10.019 10351 Z= 0.266 Chirality : 0.041 0.169 1177 Planarity : 0.003 0.030 1243 Dihedral : 14.385 100.788 1257 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 2.93 % 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: 1.26 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.80 (0.31), residues: 338 *********************** 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 110 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.845 Fit side-chains outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.8654 time to fit residues: 95.3877 Evaluate side-chains 100 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 6 average time/residue: 0.2377 time to fit residues: 2.7273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8293 moved from start: 0.8099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7663 Z= 0.163 Angle : 0.515 10.152 10351 Z= 0.262 Chirality : 0.041 0.166 1177 Planarity : 0.003 0.029 1243 Dihedral : 13.940 92.828 1257 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 940 helix: 1.37 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.73 (0.31), residues: 336 *********************** 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 99 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.810 Fit side-chains outliers start: 14 outliers final: 13 residues processed: 98 average time/residue: 0.9118 time to fit residues: 96.3604 Evaluate side-chains 95 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 1 average time/residue: 0.1124 time to fit residues: 1.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN A 512 HIS B 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.8114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7663 Z= 0.194 Angle : 0.533 11.864 10351 Z= 0.270 Chirality : 0.042 0.165 1177 Planarity : 0.003 0.029 1243 Dihedral : 13.998 92.819 1257 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 2.40 % 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: -0.04 (0.28), residues: 940 helix: 1.35 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -2.71 (0.31), residues: 338 ********************** 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 100 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.822 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 97 average time/residue: 0.9081 time to fit residues: 95.1917 Evaluate side-chains 97 residues out of total 750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 3 average time/residue: 0.4391 time to fit residues: 2.5791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 0.0470 chunk 31 optimal weight: 0.1980 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.6484 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.125326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096266 restraints weight = 8871.130| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.85 r_work: 0.2808 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 7663 Z= 0.261 Angle : 0.578 12.084 10351 Z= 0.291 Chirality : 0.043 0.163 1177 Planarity : 0.003 0.030 1243 Dihedral : 14.408 96.887 1257 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer Outliers : 2.13 % 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: -0.33 (0.28), residues: 940 helix: 1.08 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.87 (0.31), residues: 326 =============================================================================== Job complete usr+sys time: 2492.09 seconds wall clock time: 45 minutes 30.85 seconds (2730.85 seconds total)