Starting phenix.real_space_refine on Sat Jul 20 01:17:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/07_2024/7n5a_24184_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/07_2024/7n5a_24184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/07_2024/7n5a_24184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/07_2024/7n5a_24184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/07_2024/7n5a_24184_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/07_2024/7n5a_24184_neut.cif" } resolution = 3.95 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= 0.005 sd= 0.072 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 V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5886 2.51 5 N 1586 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 682": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9254 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4594 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 13, 'TRANS': 575} Chain breaks: 1 Chain: "B" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4594 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 13, 'TRANS': 575} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.90, per 1000 atoms: 0.64 Number of scatterers: 9254 At special positions: 0 Unit cell: (76.26, 92.66, 139.4, 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) V 2 22.97 S 34 16.00 P 4 15.00 Mg 2 11.99 O 1740 8.00 N 1586 7.00 C 5886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 6 sheets defined 66.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 117 through 132 Processing helix chain 'A' and resid 136 through 175 removed outlier: 3.965A pdb=" N ARG A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 4.053A pdb=" N LEU A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 243 removed outlier: 4.195A pdb=" N VAL A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.726A pdb=" N ASN A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 3.772A pdb=" N ILE A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 Processing helix chain 'A' and resid 301 through 348 removed outlier: 4.792A pdb=" N ALA A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 Processing helix chain 'A' and resid 357 through 408 removed outlier: 3.687A pdb=" N GLU A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.587A pdb=" N GLN A 413 " --> pdb=" O MET A 410 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A 414 " --> pdb=" O ASN A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.623A pdb=" N LEU A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 439 removed outlier: 3.681A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 456 removed outlier: 3.659A pdb=" N GLN A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 568 through 575 Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 617 through 633 removed outlier: 3.521A pdb=" N ALA A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 661 removed outlier: 3.762A pdb=" N LEU A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 703 removed outlier: 3.908A pdb=" N GLY A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 716 removed outlier: 3.507A pdb=" N GLN A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 132 Processing helix chain 'B' and resid 136 through 175 removed outlier: 3.966A pdb=" N ARG B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 4.053A pdb=" N LEU B 166 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 243 removed outlier: 4.196A pdb=" N VAL B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 257 through 279 removed outlier: 3.725A pdb=" N ASN B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 removed outlier: 3.772A pdb=" N ILE B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 301 through 348 removed outlier: 4.792A pdb=" N ALA B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 357 through 408 removed outlier: 3.688A pdb=" N GLU B 361 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 382 " --> pdb=" O GLN B 378 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.588A pdb=" N GLN B 413 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET B 414 " --> pdb=" O ASN B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.624A pdb=" N LEU B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 439 removed outlier: 3.681A pdb=" N ASN B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 456 removed outlier: 3.660A pdb=" N GLN B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 568 through 575 Processing helix chain 'B' and resid 581 through 592 Processing helix chain 'B' and resid 594 through 599 Processing helix chain 'B' and resid 617 through 633 removed outlier: 3.522A pdb=" N ALA B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 661 removed outlier: 3.762A pdb=" N LEU B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 removed outlier: 3.906A pdb=" N GLY B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 716 removed outlier: 3.507A pdb=" N GLN B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 496 removed outlier: 3.861A pdb=" N LEU A 495 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 486 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496 removed outlier: 3.861A pdb=" N LEU A 495 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 486 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 484 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A 533 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 558 removed outlier: 6.917A pdb=" N ILE A 683 " --> pdb=" O GLN A 694 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN A 694 " --> pdb=" O ILE A 683 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 685 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.861A pdb=" N LEU B 495 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE B 486 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.861A pdb=" N LEU B 495 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE B 486 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 484 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER B 533 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 555 through 558 removed outlier: 6.917A pdb=" N ILE B 683 " --> pdb=" O GLN B 694 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN B 694 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 685 " --> pdb=" O VAL B 692 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1719 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: 2.72 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3044 1.36 - 1.50: 2362 1.50 - 1.64: 3938 1.64 - 1.77: 0 1.77 - 1.91: 70 Bond restraints: 9414 Sorted by residual: bond pdb=" CA SER B 633 " pdb=" CB SER B 633 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.45e+00 bond pdb=" CA SER A 633 " pdb=" CB SER A 633 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.27e+00 bond pdb=" C4 ADP B 802 " pdb=" C5 ADP B 802 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C LYS A 632 " pdb=" N SER A 633 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.12e-02 7.97e+03 9.64e-01 ... (remaining 9409 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.71: 118 105.71 - 113.31: 5301 113.31 - 120.91: 4863 120.91 - 128.51: 2416 128.51 - 136.11: 48 Bond angle restraints: 12746 Sorted by residual: angle pdb=" C PRO B 559 " pdb=" N GLN B 560 " pdb=" CA GLN B 560 " ideal model delta sigma weight residual 120.44 123.99 -3.55 1.30e+00 5.92e-01 7.46e+00 angle pdb=" C PRO A 559 " pdb=" N GLN A 560 " pdb=" CA GLN A 560 " ideal model delta sigma weight residual 120.44 123.92 -3.48 1.30e+00 5.92e-01 7.15e+00 angle pdb=" N VAL A 692 " pdb=" CA VAL A 692 " pdb=" C VAL A 692 " ideal model delta sigma weight residual 110.74 113.07 -2.33 9.10e-01 1.21e+00 6.56e+00 angle pdb=" N VAL B 692 " pdb=" CA VAL B 692 " pdb=" C VAL B 692 " ideal model delta sigma weight residual 110.74 113.06 -2.32 9.10e-01 1.21e+00 6.51e+00 angle pdb=" C VAL B 609 " pdb=" CA VAL B 609 " pdb=" CB VAL B 609 " ideal model delta sigma weight residual 111.88 108.80 3.08 1.37e+00 5.33e-01 5.05e+00 ... (remaining 12741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.63: 5299 24.63 - 49.26: 299 49.26 - 73.89: 20 73.89 - 98.53: 2 98.53 - 123.16: 2 Dihedral angle restraints: 5622 sinusoidal: 2212 harmonic: 3410 Sorted by residual: dihedral pdb=" O1B ADP B 802 " pdb=" O3A ADP B 802 " pdb=" PB ADP B 802 " pdb=" PA ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 63.15 -123.16 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 63.13 -123.14 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" CA VAL B 691 " pdb=" C VAL B 691 " pdb=" N VAL B 692 " pdb=" CA VAL B 692 " ideal model delta harmonic sigma weight residual 180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 937 0.029 - 0.058: 371 0.058 - 0.087: 110 0.087 - 0.117: 60 0.117 - 0.146: 12 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CG LEU B 456 " pdb=" CB LEU B 456 " pdb=" CD1 LEU B 456 " pdb=" CD2 LEU B 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CG LEU A 456 " pdb=" CB LEU A 456 " pdb=" CD1 LEU A 456 " pdb=" CD2 LEU A 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA GLN B 413 " pdb=" N GLN B 413 " pdb=" C GLN B 413 " pdb=" CB GLN B 413 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1487 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 427 " 0.015 2.00e-02 2.50e+03 1.28e-02 2.85e+00 pdb=" CG PHE B 427 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 427 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 427 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 427 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 427 " 0.015 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE A 427 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 427 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 427 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 427 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 489 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 490 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " -0.017 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 114 2.62 - 3.19: 8974 3.19 - 3.76: 14774 3.76 - 4.33: 19539 4.33 - 4.90: 31527 Nonbonded interactions: 74928 Sorted by model distance: nonbonded pdb="MG MG A 803 " pdb=" O4 VO4 B 803 " model vdw 2.045 2.170 nonbonded pdb=" O4 VO4 A 802 " pdb="MG MG B 801 " model vdw 2.045 2.170 nonbonded pdb="MG MG A 803 " pdb=" O3B ADP B 802 " model vdw 2.066 2.170 nonbonded pdb=" O3B ADP A 801 " pdb="MG MG B 801 " model vdw 2.067 2.170 nonbonded pdb=" OG SER A 487 " pdb=" O ARG A 492 " model vdw 2.133 2.440 ... (remaining 74923 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 117 through 716) selection = (chain 'B' and resid 117 through 716) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.150 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.760 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9414 Z= 0.170 Angle : 0.613 7.847 12746 Z= 0.318 Chirality : 0.039 0.146 1490 Planarity : 0.003 0.031 1606 Dihedral : 14.007 123.157 3418 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % Favored : 99.00 % 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: 0.92 (0.25), residues: 1170 helix: 1.49 (0.20), residues: 722 sheet: 0.68 (0.61), residues: 90 loop : -1.20 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.009 0.001 HIS A 595 PHE 0.028 0.001 PHE B 427 TYR 0.008 0.001 TYR A 349 ARG 0.005 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.114 Fit side-chains REVERT: A 253 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.7030 (tpt90) REVERT: A 276 MET cc_start: 0.9332 (mmm) cc_final: 0.8855 (mmm) REVERT: B 253 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.7065 (tpt90) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.2008 time to fit residues: 24.1938 Evaluate side-chains 61 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 560 GLN B 390 GLN B 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9414 Z= 0.250 Angle : 0.647 6.009 12746 Z= 0.335 Chirality : 0.041 0.148 1490 Planarity : 0.004 0.039 1606 Dihedral : 7.367 116.063 1296 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.50 % Allowed : 8.73 % Favored : 90.76 % 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: 1.02 (0.25), residues: 1170 helix: 1.55 (0.19), residues: 732 sheet: 1.42 (0.65), residues: 86 loop : -1.41 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 132 HIS 0.006 0.002 HIS B 697 PHE 0.019 0.002 PHE A 302 TYR 0.021 0.002 TYR B 360 ARG 0.004 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.7068 (tpt90) REVERT: A 421 MET cc_start: 0.9110 (mpp) cc_final: 0.8647 (mpp) REVERT: B 253 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.7165 (tpt90) REVERT: B 276 MET cc_start: 0.9035 (mmp) cc_final: 0.8735 (mmm) REVERT: B 421 MET cc_start: 0.9145 (mpp) cc_final: 0.8683 (mpp) REVERT: B 434 ASN cc_start: 0.8949 (t0) cc_final: 0.8697 (t0) REVERT: B 672 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7034 (p90) outliers start: 5 outliers final: 1 residues processed: 72 average time/residue: 0.1992 time to fit residues: 21.3364 Evaluate side-chains 61 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 672 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 GLN ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9414 Z= 0.169 Angle : 0.594 7.769 12746 Z= 0.294 Chirality : 0.039 0.159 1490 Planarity : 0.003 0.033 1606 Dihedral : 7.131 115.225 1296 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.20 % Allowed : 10.34 % Favored : 88.45 % 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: 1.27 (0.25), residues: 1170 helix: 1.69 (0.19), residues: 734 sheet: 1.09 (0.63), residues: 88 loop : -1.07 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 132 HIS 0.004 0.001 HIS B 697 PHE 0.023 0.001 PHE A 302 TYR 0.017 0.001 TYR A 205 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.7126 (tpt90) REVERT: B 253 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.7171 (tpt90) REVERT: B 276 MET cc_start: 0.9074 (mmp) cc_final: 0.8833 (mmm) REVERT: B 289 MET cc_start: 0.6950 (mpp) cc_final: 0.6382 (mpt) REVERT: B 410 MET cc_start: 0.7935 (ppp) cc_final: 0.7612 (ppp) outliers start: 12 outliers final: 5 residues processed: 79 average time/residue: 0.2043 time to fit residues: 23.8362 Evaluate side-chains 73 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 429 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9414 Z= 0.271 Angle : 0.638 9.225 12746 Z= 0.319 Chirality : 0.042 0.253 1490 Planarity : 0.004 0.036 1606 Dihedral : 7.201 118.058 1296 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.20 % Allowed : 13.55 % Favored : 85.24 % 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: 1.21 (0.25), residues: 1170 helix: 1.69 (0.19), residues: 738 sheet: 0.96 (0.64), residues: 88 loop : -1.23 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 132 HIS 0.006 0.002 HIS A 672 PHE 0.026 0.002 PHE B 302 TYR 0.026 0.002 TYR A 360 ARG 0.004 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.7195 (tpt90) REVERT: A 672 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.7025 (p90) REVERT: B 253 ARG cc_start: 0.7464 (mtm-85) cc_final: 0.7215 (tpt90) REVERT: B 276 MET cc_start: 0.9023 (mmp) cc_final: 0.8782 (mmm) REVERT: B 289 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7292 (mpt) REVERT: B 410 MET cc_start: 0.7965 (ppp) cc_final: 0.7689 (ppp) REVERT: B 426 LEU cc_start: 0.9202 (mp) cc_final: 0.8864 (mt) REVERT: B 429 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9046 (pp) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.1854 time to fit residues: 20.5649 Evaluate side-chains 69 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 538 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 100 optimal weight: 0.0570 chunk 28 optimal weight: 2.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9414 Z= 0.187 Angle : 0.610 10.380 12746 Z= 0.298 Chirality : 0.041 0.279 1490 Planarity : 0.003 0.034 1606 Dihedral : 7.070 117.533 1296 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.51 % Allowed : 14.96 % Favored : 83.53 % 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: 1.29 (0.25), residues: 1170 helix: 1.66 (0.19), residues: 752 sheet: 0.98 (0.63), residues: 88 loop : -1.05 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 132 HIS 0.006 0.001 HIS A 672 PHE 0.030 0.001 PHE B 302 TYR 0.025 0.002 TYR A 360 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.7168 (tpt90) REVERT: A 410 MET cc_start: 0.7858 (ppp) cc_final: 0.7550 (ppp) REVERT: A 421 MET cc_start: 0.7981 (mmt) cc_final: 0.7750 (mpp) REVERT: B 253 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.7231 (tpt90) REVERT: B 289 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7313 (mpp) REVERT: B 410 MET cc_start: 0.7951 (ppp) cc_final: 0.7657 (ppp) REVERT: B 421 MET cc_start: 0.8113 (mmt) cc_final: 0.7703 (mpp) REVERT: B 426 LEU cc_start: 0.9195 (mp) cc_final: 0.8908 (mt) REVERT: B 429 LEU cc_start: 0.9335 (tt) cc_final: 0.8974 (pp) outliers start: 15 outliers final: 7 residues processed: 73 average time/residue: 0.1874 time to fit residues: 20.8329 Evaluate side-chains 67 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 538 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.0020 chunk 100 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9414 Z= 0.199 Angle : 0.612 10.841 12746 Z= 0.299 Chirality : 0.041 0.279 1490 Planarity : 0.003 0.034 1606 Dihedral : 7.019 117.607 1296 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.61 % Allowed : 17.07 % Favored : 81.33 % 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: 1.31 (0.25), residues: 1170 helix: 1.70 (0.19), residues: 750 sheet: 0.99 (0.63), residues: 88 loop : -1.09 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.007 0.001 HIS A 672 PHE 0.015 0.001 PHE A 435 TYR 0.016 0.002 TYR A 360 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7438 (mtm-85) cc_final: 0.7209 (tpt90) REVERT: B 253 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7247 (tpt90) REVERT: B 289 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7546 (mpp) REVERT: B 410 MET cc_start: 0.8017 (ppp) cc_final: 0.7722 (ppp) REVERT: B 421 MET cc_start: 0.8190 (mmt) cc_final: 0.7825 (mpp) REVERT: B 429 LEU cc_start: 0.9316 (tt) cc_final: 0.8958 (pp) outliers start: 16 outliers final: 11 residues processed: 74 average time/residue: 0.1866 time to fit residues: 21.0214 Evaluate side-chains 70 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 629 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS B 390 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9414 Z= 0.320 Angle : 0.694 11.829 12746 Z= 0.344 Chirality : 0.044 0.299 1490 Planarity : 0.004 0.035 1606 Dihedral : 7.408 123.812 1296 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.11 % Allowed : 17.57 % Favored : 80.32 % 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: 1.03 (0.25), residues: 1170 helix: 1.52 (0.18), residues: 758 sheet: 1.04 (0.63), residues: 88 loop : -1.42 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.008 0.002 HIS B 672 PHE 0.018 0.002 PHE B 630 TYR 0.017 0.002 TYR A 360 ARG 0.004 0.001 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.7269 (tpt90) REVERT: A 410 MET cc_start: 0.8142 (ppp) cc_final: 0.7820 (ppp) REVERT: B 253 ARG cc_start: 0.7523 (mtm-85) cc_final: 0.7283 (tpt90) REVERT: B 289 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7434 (mpp) REVERT: B 410 MET cc_start: 0.7982 (ppp) cc_final: 0.7673 (ppp) REVERT: B 421 MET cc_start: 0.8130 (mmt) cc_final: 0.7865 (mpp) outliers start: 21 outliers final: 8 residues processed: 77 average time/residue: 0.1815 time to fit residues: 21.3909 Evaluate side-chains 70 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 629 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9414 Z= 0.188 Angle : 0.658 12.905 12746 Z= 0.316 Chirality : 0.042 0.270 1490 Planarity : 0.003 0.034 1606 Dihedral : 7.172 119.986 1296 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.41 % Allowed : 18.88 % Favored : 79.72 % 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: 1.29 (0.25), residues: 1170 helix: 1.65 (0.19), residues: 758 sheet: 0.95 (0.63), residues: 90 loop : -1.10 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.007 0.001 HIS A 672 PHE 0.012 0.001 PHE A 486 TYR 0.016 0.001 TYR B 205 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7484 (mtm-85) cc_final: 0.7243 (tpt90) REVERT: B 253 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7276 (tpt90) REVERT: B 289 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7627 (mpp) REVERT: B 410 MET cc_start: 0.7923 (ppp) cc_final: 0.7604 (ppp) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.1856 time to fit residues: 21.7584 Evaluate side-chains 68 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 629 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 0.0170 chunk 68 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9414 Z= 0.170 Angle : 0.679 16.766 12746 Z= 0.317 Chirality : 0.042 0.241 1490 Planarity : 0.003 0.035 1606 Dihedral : 7.007 116.164 1296 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.31 % Allowed : 19.08 % Favored : 79.62 % 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: 1.20 (0.25), residues: 1170 helix: 1.54 (0.19), residues: 772 sheet: 0.96 (0.63), residues: 90 loop : -1.13 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.006 0.001 HIS A 672 PHE 0.029 0.001 PHE B 302 TYR 0.016 0.001 TYR B 205 ARG 0.005 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7237 (tpt90) REVERT: A 431 LEU cc_start: 0.9514 (pp) cc_final: 0.9283 (mp) REVERT: B 253 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.7258 (tpt90) REVERT: B 289 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7634 (mpp) REVERT: B 410 MET cc_start: 0.7881 (ppp) cc_final: 0.7537 (ppp) REVERT: B 421 MET cc_start: 0.7949 (mmt) cc_final: 0.7719 (mpp) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.1883 time to fit residues: 19.6788 Evaluate side-chains 69 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 672 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9414 Z= 0.209 Angle : 0.695 15.420 12746 Z= 0.325 Chirality : 0.042 0.245 1490 Planarity : 0.003 0.035 1606 Dihedral : 7.026 117.163 1296 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.41 % Allowed : 18.78 % Favored : 79.82 % 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: 1.14 (0.25), residues: 1170 helix: 1.54 (0.19), residues: 770 sheet: 0.96 (0.63), residues: 90 loop : -1.30 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.008 0.002 HIS A 697 PHE 0.030 0.001 PHE B 302 TYR 0.015 0.001 TYR A 205 ARG 0.004 0.000 ARG B 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 253 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.7259 (tpt90) REVERT: A 431 LEU cc_start: 0.9504 (pp) cc_final: 0.9285 (mp) REVERT: B 253 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.7285 (tpt90) REVERT: B 289 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7692 (mpp) REVERT: B 410 MET cc_start: 0.7947 (ppp) cc_final: 0.7614 (ppp) outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 0.1982 time to fit residues: 20.1114 Evaluate side-chains 71 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 672 HIS Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 672 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3103 > 50: distance: 8 - 13: 7.028 distance: 13 - 14: 10.449 distance: 14 - 15: 8.587 distance: 14 - 17: 10.227 distance: 15 - 16: 30.432 distance: 15 - 19: 34.906 distance: 17 - 18: 17.212 distance: 19 - 20: 6.440 distance: 20 - 21: 28.596 distance: 20 - 23: 17.990 distance: 21 - 22: 22.533 distance: 21 - 27: 20.558 distance: 23 - 24: 13.652 distance: 24 - 25: 12.248 distance: 24 - 26: 38.910 distance: 27 - 28: 9.733 distance: 28 - 29: 19.237 distance: 28 - 31: 26.835 distance: 29 - 30: 28.218 distance: 29 - 32: 7.682 distance: 32 - 33: 15.802 distance: 33 - 34: 20.976 distance: 33 - 36: 8.169 distance: 34 - 35: 20.451 distance: 34 - 41: 5.231 distance: 36 - 37: 4.825 distance: 37 - 38: 16.699 distance: 38 - 39: 15.709 distance: 39 - 40: 10.241 distance: 41 - 42: 14.115 distance: 41 - 47: 22.626 distance: 42 - 43: 20.645 distance: 42 - 45: 16.537 distance: 43 - 48: 23.155 distance: 45 - 46: 4.143 distance: 46 - 47: 15.308 distance: 48 - 49: 32.440 distance: 49 - 50: 6.796 distance: 49 - 52: 23.969 distance: 50 - 51: 31.120 distance: 50 - 56: 18.686 distance: 52 - 53: 24.266 distance: 53 - 54: 14.964 distance: 53 - 55: 44.080 distance: 56 - 57: 14.407 distance: 57 - 58: 12.060 distance: 57 - 60: 14.466 distance: 58 - 59: 10.864 distance: 58 - 63: 13.110 distance: 60 - 61: 3.107 distance: 60 - 62: 19.096 distance: 63 - 64: 8.380 distance: 64 - 65: 39.229 distance: 64 - 67: 16.206 distance: 65 - 66: 21.296 distance: 65 - 71: 18.990 distance: 67 - 68: 29.304 distance: 68 - 69: 15.431 distance: 68 - 70: 12.582 distance: 71 - 72: 14.378 distance: 72 - 73: 24.082 distance: 72 - 75: 14.422 distance: 73 - 74: 3.346 distance: 73 - 80: 19.585 distance: 75 - 76: 14.131 distance: 76 - 77: 12.182 distance: 77 - 78: 37.349 distance: 78 - 79: 41.455 distance: 80 - 81: 20.694 distance: 81 - 82: 29.315 distance: 82 - 83: 10.822 distance: 82 - 84: 24.014