Starting phenix.real_space_refine on Thu Mar 13 05:48:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpa_43405/03_2025/8vpa_43405.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpa_43405/03_2025/8vpa_43405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vpa_43405/03_2025/8vpa_43405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpa_43405/03_2025/8vpa_43405.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpa_43405/03_2025/8vpa_43405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpa_43405/03_2025/8vpa_43405.cif" } resolution = 3.11 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= 0.002 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 42 5.16 5 C 5618 2.51 5 N 1404 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8658 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4302 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 10, 'TRANS': 538} Chain breaks: 1 Chain: "B" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4302 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 10, 'TRANS': 538} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.02, per 1000 atoms: 0.70 Number of scatterers: 8658 At special positions: 0 Unit cell: (69.229, 95.756, 137.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 4 15.00 O 1590 8.00 N 1404 7.00 C 5618 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 - 3.00 Amino acid : True - 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: 2.39 Conformation dependent library (CDL) restraints added in 1.0 seconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 6 sheets defined 71.5% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 167 through 193 removed outlier: 3.790A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.591A pdb=" N PHE A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 251 Processing helix chain 'A' and resid 254 through 261 removed outlier: 3.917A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.167A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 305 removed outlier: 3.875A pdb=" N MET A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 354 removed outlier: 3.559A pdb=" N PHE A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 417 removed outlier: 3.573A pdb=" N LYS A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.621A pdb=" N ILE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.556A pdb=" N ARG A 472 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 549 through 553 removed outlier: 3.593A pdb=" N ILE A 553 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 601 through 607 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.702A pdb=" N ARG A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.658A pdb=" N THR A 683 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 684 " --> pdb=" O LEU A 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 680 through 684' Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.573A pdb=" N LYS A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 721 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 166 through 187 Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.570A pdb=" N ASP B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.647A pdb=" N PHE B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 251 removed outlier: 3.501A pdb=" N LEU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.841A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 Processing helix chain 'B' and resid 272 through 280 removed outlier: 4.061A pdb=" N ILE B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 305 removed outlier: 3.693A pdb=" N MET B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B 297 " --> pdb=" O MET B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 354 removed outlier: 4.853A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 418 Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 435 through 445 removed outlier: 4.350A pdb=" N VAL B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 464 Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 576 through 581 Processing helix chain 'B' and resid 590 through 599 Processing helix chain 'B' and resid 601 through 607 Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 624 through 638 Processing helix chain 'B' and resid 703 through 710 Processing helix chain 'B' and resid 712 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 502 through 509 removed outlier: 6.939A pdb=" N LYS A 503 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP A 492 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE A 505 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.422A pdb=" N ALA A 563 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP A 647 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 565 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A 644 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE A 677 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 646 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 514 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N TYR A 691 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA A 516 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU A 693 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 518 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 700 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 694 " --> pdb=" O ILE A 698 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AA4, first strand: chain 'B' and resid 502 through 509 removed outlier: 7.202A pdb=" N LYS B 503 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASP B 492 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ILE B 505 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 490 " --> pdb=" O ILE B 505 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 491 " --> pdb=" O LYS B 540 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS B 540 " --> pdb=" O VAL B 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 562 through 565 removed outlier: 6.374A pdb=" N ALA B 563 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU B 644 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ILE B 677 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 646 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B 514 " --> pdb=" O LYS B 689 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N TYR B 691 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA B 516 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU B 693 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 518 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU B 700 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS B 694 " --> pdb=" O ILE B 698 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 574 through 575 577 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2705 1.34 - 1.46: 1614 1.46 - 1.58: 4391 1.58 - 1.69: 6 1.69 - 1.81: 76 Bond restraints: 8792 Sorted by residual: bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" C GLY A 186 " pdb=" O GLY A 186 " ideal model delta sigma weight residual 1.234 1.248 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" N GLY A 186 " pdb=" CA GLY A 186 " ideal model delta sigma weight residual 1.452 1.466 -0.014 1.34e-02 5.57e+03 1.02e+00 bond pdb=" C LEU B 253 " pdb=" N PRO B 254 " ideal model delta sigma weight residual 1.331 1.343 -0.011 1.21e-02 6.83e+03 8.98e-01 ... (remaining 8787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11703 1.80 - 3.60: 105 3.60 - 5.40: 37 5.40 - 7.20: 6 7.20 - 9.00: 1 Bond angle restraints: 11852 Sorted by residual: angle pdb=" C LYS A 611 " pdb=" CA LYS A 611 " pdb=" CB LYS A 611 " ideal model delta sigma weight residual 116.54 110.32 6.22 1.15e+00 7.56e-01 2.92e+01 angle pdb=" CG1 ILE B 280 " pdb=" CB ILE B 280 " pdb=" CG2 ILE B 280 " ideal model delta sigma weight residual 110.70 101.70 9.00 3.00e+00 1.11e-01 8.99e+00 angle pdb=" C GLU B 585 " pdb=" N ASN B 586 " pdb=" CA ASN B 586 " ideal model delta sigma weight residual 122.07 125.68 -3.61 1.43e+00 4.89e-01 6.38e+00 angle pdb=" CA LYS A 611 " pdb=" C LYS A 611 " pdb=" N TYR A 612 " ideal model delta sigma weight residual 119.52 117.53 1.99 7.90e-01 1.60e+00 6.37e+00 angle pdb=" N LYS A 611 " pdb=" CA LYS A 611 " pdb=" C LYS A 611 " ideal model delta sigma weight residual 108.31 111.94 -3.63 1.52e+00 4.33e-01 5.71e+00 ... (remaining 11847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4752 17.40 - 34.79: 455 34.79 - 52.19: 91 52.19 - 69.59: 18 69.59 - 86.99: 6 Dihedral angle restraints: 5322 sinusoidal: 2148 harmonic: 3174 Sorted by residual: dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 -137.22 77.22 1 2.00e+01 2.50e-03 1.87e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 -127.04 67.04 1 2.00e+01 2.50e-03 1.46e+01 dihedral pdb=" CG ARG A 458 " pdb=" CD ARG A 458 " pdb=" NE ARG A 458 " pdb=" CZ ARG A 458 " ideal model delta sinusoidal sigma weight residual -90.00 -133.80 43.80 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1113 0.046 - 0.092: 250 0.092 - 0.138: 50 0.138 - 0.184: 0 0.184 - 0.231: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE B 280 " pdb=" CA ILE B 280 " pdb=" CG1 ILE B 280 " pdb=" CG2 ILE B 280 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE B 543 " pdb=" N ILE B 543 " pdb=" C ILE B 543 " pdb=" CB ILE B 543 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CB ILE B 480 " pdb=" CA ILE B 480 " pdb=" CG1 ILE B 480 " pdb=" CG2 ILE B 480 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1411 not shown) Planarity restraints: 1454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 328 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 329 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 446 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.31e+00 pdb=" N PRO A 447 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 446 " -0.015 5.00e-02 4.00e+02 2.24e-02 8.00e-01 pdb=" N PRO B 447 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 447 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 447 " -0.013 5.00e-02 4.00e+02 ... (remaining 1451 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1372 2.76 - 3.29: 8525 3.29 - 3.83: 14348 3.83 - 4.36: 16626 4.36 - 4.90: 29921 Nonbonded interactions: 70792 Sorted by model distance: nonbonded pdb=" O THR B 508 " pdb=" OH TYR B 691 " model vdw 2.224 3.040 nonbonded pdb=" O LEU B 610 " pdb=" OG1 THR B 614 " model vdw 2.290 3.040 nonbonded pdb=" O THR A 508 " pdb=" OH TYR A 691 " model vdw 2.297 3.040 nonbonded pdb=" ND1 HIS A 602 " pdb=" OH TYR A 612 " model vdw 2.297 3.120 nonbonded pdb=" OD1 ASN A 224 " pdb=" NH2 ARG A 227 " model vdw 2.329 3.120 ... (remaining 70787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.240 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.010 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 0.033 8792 Z= 0.171 Angle : 0.521 8.996 11852 Z= 0.269 Chirality : 0.039 0.231 1414 Planarity : 0.002 0.031 1454 Dihedral : 14.438 86.985 3274 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.35 (0.27), residues: 1090 helix: 2.42 (0.19), residues: 734 sheet: 1.44 (0.71), residues: 70 loop : -0.77 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 409 HIS 0.004 0.001 HIS A 207 PHE 0.011 0.001 PHE A 217 TYR 0.011 0.001 TYR B 225 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.872 Fit side-chains REVERT: A 457 ASN cc_start: 0.8491 (m-40) cc_final: 0.8135 (m110) REVERT: B 420 MET cc_start: 0.7975 (ttm) cc_final: 0.7748 (ttm) REVERT: B 485 ASP cc_start: 0.7504 (m-30) cc_final: 0.7223 (m-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2098 time to fit residues: 37.9189 Evaluate side-chains 111 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 622 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.140299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111568 restraints weight = 9903.766| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.73 r_work: 0.3052 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8792 Z= 0.214 Angle : 0.521 6.150 11852 Z= 0.262 Chirality : 0.041 0.196 1414 Planarity : 0.003 0.031 1454 Dihedral : 5.338 75.732 1178 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.95 % Allowed : 5.99 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.27), residues: 1090 helix: 2.40 (0.19), residues: 738 sheet: 1.09 (0.68), residues: 70 loop : -0.82 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 718 HIS 0.003 0.001 HIS A 207 PHE 0.017 0.001 PHE A 604 TYR 0.011 0.001 TYR B 225 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.815 Fit side-chains REVERT: A 155 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5396 (mtm) REVERT: A 457 ASN cc_start: 0.8552 (m-40) cc_final: 0.8116 (m110) REVERT: B 208 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7488 (mt) REVERT: B 589 MET cc_start: 0.8785 (tpp) cc_final: 0.8513 (tpp) REVERT: B 603 ASP cc_start: 0.8370 (m-30) cc_final: 0.8145 (m-30) REVERT: B 622 ASN cc_start: 0.8545 (t0) cc_final: 0.8282 (t0) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.1968 time to fit residues: 35.0811 Evaluate side-chains 123 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 456 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110924 restraints weight = 10161.684| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.74 r_work: 0.3057 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8792 Z= 0.184 Angle : 0.498 6.694 11852 Z= 0.249 Chirality : 0.040 0.223 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.263 70.865 1178 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.26 % Allowed : 7.35 % Favored : 91.39 % 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: 2.40 (0.27), residues: 1090 helix: 2.59 (0.19), residues: 732 sheet: 0.96 (0.66), residues: 70 loop : -0.97 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 207 PHE 0.012 0.001 PHE A 604 TYR 0.010 0.001 TYR A 226 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.947 Fit side-chains REVERT: A 248 SER cc_start: 0.8233 (m) cc_final: 0.7939 (m) REVERT: A 457 ASN cc_start: 0.8536 (m-40) cc_final: 0.8084 (m110) REVERT: B 166 LYS cc_start: 0.7205 (tttm) cc_final: 0.6736 (mtpp) REVERT: B 208 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7462 (mt) REVERT: B 589 MET cc_start: 0.8763 (tpp) cc_final: 0.8477 (tpp) REVERT: B 603 ASP cc_start: 0.8373 (m-30) cc_final: 0.8151 (m-30) outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.2358 time to fit residues: 43.0924 Evaluate side-chains 126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 456 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112979 restraints weight = 9941.102| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.72 r_work: 0.3071 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8792 Z= 0.166 Angle : 0.487 7.105 11852 Z= 0.242 Chirality : 0.040 0.231 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.190 66.647 1178 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.16 % Allowed : 9.45 % Favored : 89.39 % 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: 2.49 (0.26), residues: 1090 helix: 2.68 (0.19), residues: 732 sheet: 0.91 (0.65), residues: 70 loop : -1.00 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 207 PHE 0.011 0.001 PHE A 217 TYR 0.010 0.001 TYR B 225 ARG 0.002 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.007 Fit side-chains REVERT: A 190 ILE cc_start: 0.6494 (mt) cc_final: 0.6282 (mt) REVERT: A 248 SER cc_start: 0.8205 (m) cc_final: 0.7907 (m) REVERT: A 457 ASN cc_start: 0.8513 (m-40) cc_final: 0.8101 (m-40) REVERT: A 584 ASN cc_start: 0.7053 (t0) cc_final: 0.6752 (t0) REVERT: B 166 LYS cc_start: 0.7159 (tttm) cc_final: 0.6696 (mtpp) REVERT: B 208 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7468 (mt) REVERT: B 589 MET cc_start: 0.8751 (tpp) cc_final: 0.8459 (tpp) REVERT: B 603 ASP cc_start: 0.8371 (m-30) cc_final: 0.8150 (m-30) REVERT: B 604 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8026 (p90) outliers start: 11 outliers final: 8 residues processed: 130 average time/residue: 0.2233 time to fit residues: 39.8515 Evaluate side-chains 131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 710 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 42 optimal weight: 0.0370 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN B 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.145884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118000 restraints weight = 10027.204| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.73 r_work: 0.3128 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8792 Z= 0.137 Angle : 0.478 7.187 11852 Z= 0.235 Chirality : 0.039 0.207 1414 Planarity : 0.002 0.027 1454 Dihedral : 5.090 57.285 1178 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.00 % Allowed : 9.35 % Favored : 88.66 % 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: 2.52 (0.26), residues: 1090 helix: 2.68 (0.19), residues: 744 sheet: 0.83 (0.64), residues: 70 loop : -1.04 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 409 HIS 0.003 0.001 HIS A 207 PHE 0.010 0.001 PHE A 217 TYR 0.009 0.001 TYR B 179 ARG 0.002 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.995 Fit side-chains REVERT: A 155 MET cc_start: 0.6192 (tpt) cc_final: 0.5248 (mtm) REVERT: A 248 SER cc_start: 0.8123 (m) cc_final: 0.7827 (m) REVERT: A 457 ASN cc_start: 0.8488 (m-40) cc_final: 0.8084 (m-40) REVERT: A 584 ASN cc_start: 0.7013 (t0) cc_final: 0.6720 (t0) REVERT: B 166 LYS cc_start: 0.7132 (tttm) cc_final: 0.6747 (mtpp) REVERT: B 208 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7463 (mt) REVERT: B 293 MET cc_start: 0.8128 (mtt) cc_final: 0.7870 (mtt) REVERT: B 589 MET cc_start: 0.8729 (tpp) cc_final: 0.8449 (tpp) REVERT: B 603 ASP cc_start: 0.8348 (m-30) cc_final: 0.8116 (m-30) REVERT: B 604 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.8039 (p90) REVERT: B 605 ILE cc_start: 0.8253 (mt) cc_final: 0.8001 (mm) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.2138 time to fit residues: 39.1093 Evaluate side-chains 130 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 710 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.145549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.117983 restraints weight = 9907.955| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.67 r_work: 0.3083 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8792 Z= 0.187 Angle : 0.493 8.278 11852 Z= 0.243 Chirality : 0.040 0.228 1414 Planarity : 0.002 0.027 1454 Dihedral : 5.124 57.092 1178 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 10.40 % Favored : 87.71 % 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: 2.50 (0.26), residues: 1090 helix: 2.75 (0.19), residues: 732 sheet: 1.33 (0.77), residues: 50 loop : -1.14 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 249 PHE 0.012 0.001 PHE A 604 TYR 0.010 0.001 TYR A 225 ARG 0.002 0.000 ARG B 494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.943 Fit side-chains REVERT: A 155 MET cc_start: 0.6254 (tpt) cc_final: 0.5284 (mtm) REVERT: A 248 SER cc_start: 0.8169 (m) cc_final: 0.7881 (m) REVERT: A 457 ASN cc_start: 0.8505 (m-40) cc_final: 0.8088 (m-40) REVERT: A 584 ASN cc_start: 0.7087 (t0) cc_final: 0.6834 (t0) REVERT: B 166 LYS cc_start: 0.7163 (tttm) cc_final: 0.6770 (mtpp) REVERT: B 208 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7444 (mt) REVERT: B 589 MET cc_start: 0.8735 (tpp) cc_final: 0.8471 (tpp) REVERT: B 603 ASP cc_start: 0.8371 (m-30) cc_final: 0.8139 (m-30) REVERT: B 604 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8114 (p90) outliers start: 18 outliers final: 16 residues processed: 126 average time/residue: 0.2125 time to fit residues: 37.3852 Evaluate side-chains 132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 710 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN B 567 GLN B 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.144225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116361 restraints weight = 10036.212| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.69 r_work: 0.3059 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8792 Z= 0.211 Angle : 0.506 8.397 11852 Z= 0.250 Chirality : 0.040 0.220 1414 Planarity : 0.002 0.027 1454 Dihedral : 5.170 58.762 1178 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.42 % Allowed : 11.24 % Favored : 86.34 % 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: 2.42 (0.26), residues: 1090 helix: 2.69 (0.19), residues: 734 sheet: 1.33 (0.77), residues: 50 loop : -1.20 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 409 HIS 0.003 0.001 HIS A 249 PHE 0.013 0.001 PHE A 604 TYR 0.011 0.001 TYR A 225 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.931 Fit side-chains REVERT: A 155 MET cc_start: 0.6271 (tpt) cc_final: 0.5311 (mtm) REVERT: A 248 SER cc_start: 0.8234 (m) cc_final: 0.7935 (m) REVERT: A 457 ASN cc_start: 0.8539 (m-40) cc_final: 0.8243 (m110) REVERT: A 584 ASN cc_start: 0.7074 (t0) cc_final: 0.6827 (t0) REVERT: B 166 LYS cc_start: 0.7176 (tttm) cc_final: 0.6713 (mtpp) REVERT: B 208 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7470 (mt) REVERT: B 603 ASP cc_start: 0.8407 (m-30) cc_final: 0.8186 (m-30) REVERT: B 604 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8176 (p90) outliers start: 23 outliers final: 15 residues processed: 131 average time/residue: 0.2116 time to fit residues: 38.1903 Evaluate side-chains 131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 710 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.140138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111485 restraints weight = 10241.862| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.76 r_work: 0.3064 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8792 Z= 0.177 Angle : 0.502 8.815 11852 Z= 0.249 Chirality : 0.040 0.198 1414 Planarity : 0.002 0.027 1454 Dihedral : 5.182 57.532 1178 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.79 % Allowed : 11.66 % Favored : 86.55 % 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: 2.37 (0.26), residues: 1090 helix: 2.64 (0.19), residues: 744 sheet: 1.34 (0.77), residues: 50 loop : -1.33 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 249 PHE 0.011 0.001 PHE A 217 TYR 0.010 0.001 TYR A 225 ARG 0.002 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.943 Fit side-chains REVERT: A 155 MET cc_start: 0.6215 (tpt) cc_final: 0.5245 (mtm) REVERT: A 190 ILE cc_start: 0.6520 (mt) cc_final: 0.6300 (mt) REVERT: A 248 SER cc_start: 0.8194 (m) cc_final: 0.7895 (m) REVERT: A 457 ASN cc_start: 0.8520 (m-40) cc_final: 0.8227 (m110) REVERT: A 584 ASN cc_start: 0.7060 (t0) cc_final: 0.6806 (t0) REVERT: A 586 ASN cc_start: 0.6694 (m110) cc_final: 0.6275 (t0) REVERT: B 166 LYS cc_start: 0.7111 (tttm) cc_final: 0.6644 (mtpp) REVERT: B 208 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7405 (mt) REVERT: B 603 ASP cc_start: 0.8389 (m-30) cc_final: 0.8167 (m-30) REVERT: B 604 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (p90) outliers start: 17 outliers final: 14 residues processed: 126 average time/residue: 0.2124 time to fit residues: 37.2091 Evaluate side-chains 132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 710 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 34 optimal weight: 0.0270 chunk 85 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114895 restraints weight = 10140.800| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.70 r_work: 0.3094 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8792 Z= 0.149 Angle : 0.488 9.258 11852 Z= 0.241 Chirality : 0.039 0.155 1414 Planarity : 0.002 0.027 1454 Dihedral : 5.151 59.182 1178 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.89 % Allowed : 11.66 % Favored : 86.45 % 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: 2.47 (0.26), residues: 1090 helix: 2.71 (0.19), residues: 744 sheet: 1.34 (0.79), residues: 50 loop : -1.30 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 409 HIS 0.003 0.001 HIS A 207 PHE 0.010 0.001 PHE A 217 TYR 0.009 0.001 TYR A 225 ARG 0.002 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.965 Fit side-chains REVERT: A 155 MET cc_start: 0.6270 (tpt) cc_final: 0.5274 (mtm) REVERT: A 248 SER cc_start: 0.8135 (m) cc_final: 0.7857 (m) REVERT: A 457 ASN cc_start: 0.8508 (m-40) cc_final: 0.8222 (m110) REVERT: A 584 ASN cc_start: 0.7117 (t0) cc_final: 0.6158 (p0) REVERT: B 166 LYS cc_start: 0.7130 (tttm) cc_final: 0.6684 (mtpp) REVERT: B 208 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7414 (mt) REVERT: B 293 MET cc_start: 0.8161 (mtt) cc_final: 0.7916 (mtt) REVERT: B 560 LYS cc_start: 0.8723 (mttt) cc_final: 0.7876 (mtpp) REVERT: B 589 MET cc_start: 0.8718 (tpp) cc_final: 0.8445 (tpp) REVERT: B 603 ASP cc_start: 0.8353 (m-30) cc_final: 0.8125 (m-30) REVERT: B 604 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8178 (p90) outliers start: 18 outliers final: 15 residues processed: 129 average time/residue: 0.2150 time to fit residues: 38.4845 Evaluate side-chains 134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.144993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117216 restraints weight = 10032.303| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.70 r_work: 0.3091 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8792 Z= 0.159 Angle : 0.492 10.374 11852 Z= 0.243 Chirality : 0.039 0.137 1414 Planarity : 0.002 0.027 1454 Dihedral : 5.041 53.253 1178 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.68 % Allowed : 12.29 % Favored : 86.03 % 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: 2.48 (0.26), residues: 1090 helix: 2.72 (0.19), residues: 744 sheet: 1.34 (0.78), residues: 50 loop : -1.29 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 409 HIS 0.003 0.001 HIS A 249 PHE 0.010 0.001 PHE A 217 TYR 0.010 0.001 TYR A 225 ARG 0.003 0.000 ARG B 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.052 Fit side-chains REVERT: A 155 MET cc_start: 0.6273 (tpt) cc_final: 0.5272 (mtm) REVERT: A 248 SER cc_start: 0.8144 (m) cc_final: 0.7866 (m) REVERT: A 457 ASN cc_start: 0.8524 (m-40) cc_final: 0.8234 (m110) REVERT: A 584 ASN cc_start: 0.7128 (t0) cc_final: 0.6224 (p0) REVERT: B 166 LYS cc_start: 0.7125 (tttm) cc_final: 0.6672 (mtpp) REVERT: B 208 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7392 (mt) REVERT: B 293 MET cc_start: 0.8163 (mtt) cc_final: 0.7922 (mtt) REVERT: B 560 LYS cc_start: 0.8723 (mttt) cc_final: 0.7861 (mtpp) REVERT: B 589 MET cc_start: 0.8713 (tpp) cc_final: 0.8450 (tpp) REVERT: B 603 ASP cc_start: 0.8360 (m-30) cc_final: 0.8128 (m-30) REVERT: B 604 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8171 (p90) outliers start: 16 outliers final: 14 residues processed: 128 average time/residue: 0.2274 time to fit residues: 39.7852 Evaluate side-chains 133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 503 LYS Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.141119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112846 restraints weight = 10071.446| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.70 r_work: 0.3080 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8792 Z= 0.167 Angle : 0.494 10.421 11852 Z= 0.244 Chirality : 0.039 0.135 1414 Planarity : 0.002 0.027 1454 Dihedral : 5.000 53.572 1178 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.79 % Allowed : 12.29 % Favored : 85.92 % 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: 2.46 (0.26), residues: 1090 helix: 2.71 (0.19), residues: 744 sheet: 1.34 (0.78), residues: 50 loop : -1.30 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 409 HIS 0.003 0.001 HIS A 249 PHE 0.011 0.001 PHE A 604 TYR 0.010 0.001 TYR A 225 ARG 0.002 0.000 ARG B 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4441.33 seconds wall clock time: 78 minutes 43.57 seconds (4723.57 seconds total)