Starting phenix.real_space_refine on Wed Feb 4 02:59:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpa_43405/02_2026/8vpa_43405.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpa_43405/02_2026/8vpa_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vpa_43405/02_2026/8vpa_43405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpa_43405/02_2026/8vpa_43405.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vpa_43405/02_2026/8vpa_43405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpa_43405/02_2026/8vpa_43405.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 1.54, per 1000 atoms: 0.18 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: 0.82 Conformation dependent library (CDL) restraints added in 274.1 milliseconds 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: 0.40 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: 1.37 Time building geometry restraints manager: 1.07 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: 0.01 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.030 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- 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= 0.125 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG A 277 TYR 0.011 0.001 TYR B 225 PHE 0.011 0.001 PHE A 217 TRP 0.002 0.001 TRP B 409 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8792) covalent geometry : angle 0.52108 (11852) hydrogen bonds : bond 0.12931 ( 577) hydrogen bonds : angle 4.73747 ( 1695) *********************** 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 : 0.345 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: 0.0721 time to fit residues: 13.2001 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 : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- 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 = 0.140233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111384 restraints weight = 10077.837| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.75 r_work: 0.3039 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8792 Z= 0.146 Angle : 0.522 6.187 11852 Z= 0.262 Chirality : 0.041 0.200 1414 Planarity : 0.003 0.031 1454 Dihedral : 5.340 75.727 1178 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.95 % Allowed : 6.20 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.27), residues: 1090 helix: 2.39 (0.19), residues: 738 sheet: 1.07 (0.68), residues: 70 loop : -0.82 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.011 0.001 TYR B 225 PHE 0.017 0.001 PHE A 604 TRP 0.003 0.001 TRP A 718 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8792) covalent geometry : angle 0.52248 (11852) hydrogen bonds : bond 0.05187 ( 577) hydrogen bonds : angle 3.98565 ( 1695) *********************** 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 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.315 Fit side-chains REVERT: A 155 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5397 (mtm) REVERT: A 158 PHE cc_start: 0.6393 (m-80) cc_final: 0.6193 (m-80) REVERT: A 457 ASN cc_start: 0.8559 (m-40) cc_final: 0.8134 (m110) REVERT: B 208 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7491 (mt) REVERT: B 244 MET cc_start: 0.8119 (mmm) cc_final: 0.7891 (mmm) REVERT: B 589 MET cc_start: 0.8783 (tpp) cc_final: 0.8509 (tpp) REVERT: B 603 ASP cc_start: 0.8369 (m-30) cc_final: 0.8148 (m-30) REVERT: B 622 ASN cc_start: 0.8541 (t0) cc_final: 0.8274 (t0) outliers start: 9 outliers final: 7 residues processed: 124 average time/residue: 0.0666 time to fit residues: 11.7925 Evaluate side-chains 122 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 39 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN B 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109982 restraints weight = 9955.601| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.72 r_work: 0.3046 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0843 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= 0.141 Angle : 0.506 6.065 11852 Z= 0.253 Chirality : 0.040 0.195 1414 Planarity : 0.003 0.029 1454 Dihedral : 5.288 71.998 1178 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.37 % Allowed : 7.56 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.27), residues: 1090 helix: 2.52 (0.19), residues: 734 sheet: 0.95 (0.66), residues: 70 loop : -1.00 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.011 0.001 TYR A 226 PHE 0.013 0.001 PHE A 604 TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8792) covalent geometry : angle 0.50556 (11852) hydrogen bonds : bond 0.04999 ( 577) hydrogen bonds : angle 3.85345 ( 1695) *********************** 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 134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.220 Fit side-chains REVERT: A 158 PHE cc_start: 0.6422 (m-80) cc_final: 0.6193 (m-80) REVERT: A 248 SER cc_start: 0.8247 (m) cc_final: 0.7958 (m) REVERT: A 457 ASN cc_start: 0.8540 (m-40) cc_final: 0.8092 (m110) REVERT: B 166 LYS cc_start: 0.7207 (tttm) cc_final: 0.6740 (mtpp) REVERT: B 208 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7478 (mt) REVERT: B 244 MET cc_start: 0.8129 (mmm) cc_final: 0.7901 (mmm) REVERT: B 589 MET cc_start: 0.8767 (tpp) cc_final: 0.8510 (tpp) REVERT: B 603 ASP cc_start: 0.8364 (m-30) cc_final: 0.8142 (m-30) outliers start: 13 outliers final: 8 residues processed: 131 average time/residue: 0.0776 time to fit residues: 14.1374 Evaluate side-chains 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 105 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.141779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113211 restraints weight = 10203.760| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.75 r_work: 0.3058 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8792 Z= 0.124 Angle : 0.489 5.992 11852 Z= 0.244 Chirality : 0.040 0.204 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.224 68.274 1178 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 9.56 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.26), residues: 1090 helix: 2.64 (0.19), residues: 732 sheet: 0.91 (0.65), residues: 70 loop : -1.07 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 472 TYR 0.010 0.001 TYR A 226 PHE 0.011 0.001 PHE A 217 TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8792) covalent geometry : angle 0.48897 (11852) hydrogen bonds : bond 0.04730 ( 577) hydrogen bonds : angle 3.74484 ( 1695) *********************** 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 129 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.248 Fit side-chains REVERT: A 158 PHE cc_start: 0.6429 (m-80) cc_final: 0.6225 (m-80) REVERT: A 248 SER cc_start: 0.8209 (m) cc_final: 0.7913 (m) REVERT: A 457 ASN cc_start: 0.8544 (m-40) cc_final: 0.8128 (m-40) REVERT: A 584 ASN cc_start: 0.7058 (t0) cc_final: 0.6750 (t0) REVERT: B 166 LYS cc_start: 0.7165 (tttm) cc_final: 0.6703 (mtpp) REVERT: B 208 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7465 (mt) REVERT: B 244 MET cc_start: 0.8110 (mmm) cc_final: 0.7878 (mmm) REVERT: B 494 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8542 (ptp-110) REVERT: B 589 MET cc_start: 0.8753 (tpp) cc_final: 0.8488 (tpp) REVERT: B 603 ASP cc_start: 0.8372 (m-30) cc_final: 0.8157 (m-30) REVERT: B 604 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8015 (p90) outliers start: 12 outliers final: 8 residues processed: 125 average time/residue: 0.0831 time to fit residues: 14.4114 Evaluate side-chains 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 494 ARG 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 24 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 83 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.142011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113694 restraints weight = 9998.526| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.73 r_work: 0.3049 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8792 Z= 0.134 Angle : 0.498 6.070 11852 Z= 0.248 Chirality : 0.040 0.203 1414 Planarity : 0.003 0.029 1454 Dihedral : 5.213 65.545 1178 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.10 % Allowed : 9.66 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.26), residues: 1090 helix: 2.63 (0.19), residues: 734 sheet: 0.83 (0.64), residues: 70 loop : -1.11 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 269 TYR 0.011 0.001 TYR A 226 PHE 0.012 0.001 PHE A 604 TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8792) covalent geometry : angle 0.49786 (11852) hydrogen bonds : bond 0.04803 ( 577) hydrogen bonds : angle 3.70029 ( 1695) *********************** 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 135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.241 Fit side-chains REVERT: A 158 PHE cc_start: 0.6430 (m-80) cc_final: 0.6229 (m-80) REVERT: A 248 SER cc_start: 0.8223 (m) cc_final: 0.7928 (m) REVERT: A 457 ASN cc_start: 0.8514 (m-40) cc_final: 0.8090 (m-40) REVERT: A 584 ASN cc_start: 0.7025 (t0) cc_final: 0.6721 (t0) REVERT: B 166 LYS cc_start: 0.7148 (tttm) cc_final: 0.6692 (mtpp) REVERT: B 208 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7460 (mt) REVERT: B 244 MET cc_start: 0.8140 (mmm) cc_final: 0.7882 (mmm) REVERT: B 589 MET cc_start: 0.8749 (tpp) cc_final: 0.8475 (tpp) REVERT: B 603 ASP cc_start: 0.8399 (m-30) cc_final: 0.8186 (m-30) REVERT: B 604 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8154 (p90) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.0771 time to fit residues: 13.9357 Evaluate side-chains 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 0.7980 chunk 97 optimal weight: 0.0570 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113572 restraints weight = 10026.791| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.72 r_work: 0.3056 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1103 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= 0.117 Angle : 0.487 8.636 11852 Z= 0.243 Chirality : 0.040 0.237 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.178 62.866 1178 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.00 % Allowed : 10.92 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.26), residues: 1090 helix: 2.60 (0.19), residues: 744 sheet: 0.80 (0.64), residues: 70 loop : -1.18 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 269 TYR 0.010 0.001 TYR A 226 PHE 0.011 0.001 PHE A 217 TRP 0.002 0.001 TRP A 409 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8792) covalent geometry : angle 0.48718 (11852) hydrogen bonds : bond 0.04569 ( 577) hydrogen bonds : angle 3.64042 ( 1695) *********************** 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 134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.308 Fit side-chains REVERT: A 190 ILE cc_start: 0.6522 (mt) cc_final: 0.6304 (mt) REVERT: A 248 SER cc_start: 0.8191 (m) cc_final: 0.7889 (m) REVERT: A 457 ASN cc_start: 0.8505 (m-40) cc_final: 0.8074 (m-40) REVERT: A 584 ASN cc_start: 0.7016 (t0) cc_final: 0.6755 (t0) REVERT: B 166 LYS cc_start: 0.7134 (tttm) cc_final: 0.6662 (mtpp) REVERT: B 208 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7455 (mt) REVERT: B 244 MET cc_start: 0.8130 (mmm) cc_final: 0.7877 (mmm) REVERT: B 589 MET cc_start: 0.8726 (tpp) cc_final: 0.8451 (tpp) REVERT: B 603 ASP cc_start: 0.8370 (m-30) cc_final: 0.8152 (m-30) REVERT: B 604 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (p90) outliers start: 19 outliers final: 15 residues processed: 127 average time/residue: 0.0848 time to fit residues: 14.7697 Evaluate side-chains 130 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.139399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110841 restraints weight = 10227.936| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.75 r_work: 0.3056 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8792 Z= 0.127 Angle : 0.495 8.639 11852 Z= 0.246 Chirality : 0.040 0.228 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.181 62.324 1178 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.00 % Allowed : 10.92 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.26), residues: 1090 helix: 2.69 (0.19), residues: 732 sheet: 1.30 (0.77), residues: 50 loop : -1.26 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 494 TYR 0.010 0.001 TYR A 225 PHE 0.011 0.001 PHE A 604 TRP 0.002 0.001 TRP A 409 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8792) covalent geometry : angle 0.49497 (11852) hydrogen bonds : bond 0.04640 ( 577) hydrogen bonds : angle 3.63295 ( 1695) *********************** 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 136 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.220 Fit side-chains REVERT: A 190 ILE cc_start: 0.6566 (mt) cc_final: 0.6345 (mt) REVERT: A 248 SER cc_start: 0.8220 (m) cc_final: 0.7911 (m) REVERT: A 457 ASN cc_start: 0.8534 (m-40) cc_final: 0.8098 (m-40) REVERT: A 584 ASN cc_start: 0.7063 (t0) cc_final: 0.6803 (t0) REVERT: A 586 ASN cc_start: 0.6756 (m110) cc_final: 0.6309 (t0) REVERT: B 166 LYS cc_start: 0.7129 (tttm) cc_final: 0.6661 (mtpp) REVERT: B 208 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7437 (mt) REVERT: B 244 MET cc_start: 0.8153 (mmm) cc_final: 0.7833 (mmm) REVERT: B 603 ASP cc_start: 0.8392 (m-30) cc_final: 0.8179 (m-30) REVERT: B 604 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8139 (p90) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.0809 time to fit residues: 14.6862 Evaluate side-chains 130 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.143314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115699 restraints weight = 9979.487| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.65 r_work: 0.3084 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8792 Z= 0.123 Angle : 0.497 7.625 11852 Z= 0.248 Chirality : 0.040 0.175 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.182 59.141 1178 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.00 % Allowed : 11.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.26), residues: 1090 helix: 2.60 (0.19), residues: 744 sheet: 1.31 (0.78), residues: 50 loop : -1.34 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 472 TYR 0.010 0.001 TYR A 225 PHE 0.011 0.001 PHE A 217 TRP 0.002 0.001 TRP A 409 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8792) covalent geometry : angle 0.49675 (11852) hydrogen bonds : bond 0.04553 ( 577) hydrogen bonds : angle 3.59836 ( 1695) *********************** 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 135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.284 Fit side-chains REVERT: A 155 MET cc_start: 0.6224 (tpt) cc_final: 0.5237 (mtm) REVERT: A 190 ILE cc_start: 0.6512 (mt) cc_final: 0.6289 (mt) REVERT: A 248 SER cc_start: 0.8205 (m) cc_final: 0.7898 (m) REVERT: A 457 ASN cc_start: 0.8512 (m-40) cc_final: 0.8215 (m110) REVERT: A 584 ASN cc_start: 0.7099 (t0) cc_final: 0.6850 (t0) REVERT: A 604 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7940 (p90) REVERT: B 166 LYS cc_start: 0.7151 (tttm) cc_final: 0.6690 (mtpp) REVERT: B 208 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7418 (mt) REVERT: B 244 MET cc_start: 0.8159 (mmm) cc_final: 0.7838 (mmm) REVERT: B 560 LYS cc_start: 0.8737 (mttt) cc_final: 0.7898 (mtpp) REVERT: B 603 ASP cc_start: 0.8387 (m-30) cc_final: 0.8177 (m-30) REVERT: B 604 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8145 (p90) outliers start: 19 outliers final: 16 residues processed: 127 average time/residue: 0.0786 time to fit residues: 13.8803 Evaluate side-chains 132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 604 PHE 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 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 48 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.141309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113038 restraints weight = 10086.177| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.73 r_work: 0.3011 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8792 Z= 0.172 Angle : 0.537 7.489 11852 Z= 0.269 Chirality : 0.041 0.157 1414 Planarity : 0.003 0.028 1454 Dihedral : 5.281 64.858 1178 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.00 % Allowed : 11.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.26), residues: 1090 helix: 2.55 (0.19), residues: 734 sheet: 1.29 (0.78), residues: 50 loop : -1.35 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 472 TYR 0.012 0.002 TYR A 226 PHE 0.016 0.002 PHE A 604 TRP 0.004 0.001 TRP B 409 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8792) covalent geometry : angle 0.53740 (11852) hydrogen bonds : bond 0.05109 ( 577) hydrogen bonds : angle 3.71964 ( 1695) *********************** 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 128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.279 Fit side-chains REVERT: A 155 MET cc_start: 0.6249 (tpt) cc_final: 0.5264 (mtm) REVERT: A 248 SER cc_start: 0.8296 (m) cc_final: 0.8011 (m) REVERT: A 457 ASN cc_start: 0.8539 (m-40) cc_final: 0.8090 (m-40) REVERT: A 584 ASN cc_start: 0.7106 (t0) cc_final: 0.6848 (t0) REVERT: B 166 LYS cc_start: 0.7179 (tttm) cc_final: 0.6709 (mtpp) REVERT: B 208 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7420 (mt) REVERT: B 244 MET cc_start: 0.8251 (mmm) cc_final: 0.7852 (mmm) REVERT: B 560 LYS cc_start: 0.8760 (mttt) cc_final: 0.7917 (mtpp) REVERT: B 603 ASP cc_start: 0.8418 (m-30) cc_final: 0.8215 (m-30) outliers start: 19 outliers final: 16 residues processed: 122 average time/residue: 0.0819 time to fit residues: 13.7634 Evaluate side-chains 126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 420 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 503 LYS 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 85 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.139723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111444 restraints weight = 10148.634| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.70 r_work: 0.3047 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8792 Z= 0.131 Angle : 0.506 6.372 11852 Z= 0.253 Chirality : 0.040 0.137 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.253 63.721 1178 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.00 % Allowed : 11.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.26), residues: 1090 helix: 2.50 (0.19), residues: 746 sheet: 1.27 (0.78), residues: 50 loop : -1.39 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 494 TYR 0.010 0.001 TYR A 226 PHE 0.025 0.001 PHE B 604 TRP 0.002 0.001 TRP B 409 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8792) covalent geometry : angle 0.50580 (11852) hydrogen bonds : bond 0.04757 ( 577) hydrogen bonds : angle 3.65199 ( 1695) ********************** 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 131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.322 Fit side-chains REVERT: A 155 MET cc_start: 0.6314 (tpt) cc_final: 0.5296 (mtm) REVERT: A 248 SER cc_start: 0.8260 (m) cc_final: 0.7968 (m) REVERT: A 457 ASN cc_start: 0.8543 (m-40) cc_final: 0.8241 (m110) REVERT: A 584 ASN cc_start: 0.7107 (t0) cc_final: 0.6174 (p0) REVERT: B 166 LYS cc_start: 0.7171 (tttm) cc_final: 0.6715 (mtpp) REVERT: B 208 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7461 (mt) REVERT: B 244 MET cc_start: 0.8214 (mmm) cc_final: 0.7843 (mmm) REVERT: B 560 LYS cc_start: 0.8771 (mttt) cc_final: 0.7934 (mtpp) REVERT: B 603 ASP cc_start: 0.8422 (m-30) cc_final: 0.8207 (m-30) outliers start: 19 outliers final: 16 residues processed: 125 average time/residue: 0.0871 time to fit residues: 14.8541 Evaluate side-chains 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.137462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.108969 restraints weight = 10153.899| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.70 r_work: 0.3030 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8792 Z= 0.152 Angle : 0.526 7.713 11852 Z= 0.263 Chirality : 0.041 0.160 1414 Planarity : 0.003 0.028 1454 Dihedral : 5.289 64.452 1178 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.26), residues: 1090 helix: 2.57 (0.19), residues: 734 sheet: 1.23 (0.78), residues: 50 loop : -1.33 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 277 TYR 0.011 0.001 TYR A 226 PHE 0.033 0.001 PHE B 604 TRP 0.003 0.001 TRP B 409 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8792) covalent geometry : angle 0.52618 (11852) hydrogen bonds : bond 0.04967 ( 577) hydrogen bonds : angle 3.69896 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.79 seconds wall clock time: 32 minutes 52.55 seconds (1972.55 seconds total)