Starting phenix.real_space_refine on Fri Nov 15 09:08:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpa_43405/11_2024/8vpa_43405.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpa_43405/11_2024/8vpa_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpa_43405/11_2024/8vpa_43405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpa_43405/11_2024/8vpa_43405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpa_43405/11_2024/8vpa_43405.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpa_43405/11_2024/8vpa_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-5513/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: 6.42, per 1000 atoms: 0.74 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 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: 1.06 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: 2.77 Time building geometry restraints manager: 2.55 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: 0.00 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: 3.380 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: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.720 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- 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= 0.171 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 : 0.997 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: 0.2051 time to fit residues: 37.5488 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 : 1.014 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.989 Fit side-chains REVERT: A 155 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5367 (mtm) REVERT: A 457 ASN cc_start: 0.8505 (m-40) cc_final: 0.8042 (m110) REVERT: B 208 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7453 (mt) REVERT: B 244 MET cc_start: 0.7975 (mmm) cc_final: 0.7754 (mmm) REVERT: B 589 MET cc_start: 0.8740 (tpp) cc_final: 0.8454 (tpp) REVERT: B 603 ASP cc_start: 0.8261 (m-30) cc_final: 0.8018 (m-30) REVERT: B 622 ASN cc_start: 0.8444 (t0) cc_final: 0.8161 (t0) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.1955 time to fit residues: 34.8052 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 : 1.028 ------------------------------------------------------------------------------- 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 54 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0856 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= 0.214 Angle : 0.509 6.789 11852 Z= 0.255 Chirality : 0.040 0.216 1414 Planarity : 0.003 0.030 1454 Dihedral : 5.297 72.202 1178 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.26 % Allowed : 7.67 % 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 (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: 2.32 (0.27), residues: 1090 helix: 2.51 (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 TRP 0.002 0.001 TRP B 409 HIS 0.003 0.001 HIS A 207 PHE 0.013 0.001 PHE A 604 TYR 0.011 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 133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.994 Fit side-chains REVERT: A 248 SER cc_start: 0.8242 (m) cc_final: 0.7913 (m) REVERT: A 457 ASN cc_start: 0.8500 (m-40) cc_final: 0.8073 (m-40) REVERT: B 166 LYS cc_start: 0.7219 (tttm) cc_final: 0.6760 (mtpp) REVERT: B 208 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7437 (mt) REVERT: B 244 MET cc_start: 0.7986 (mmm) cc_final: 0.7749 (mmm) REVERT: B 589 MET cc_start: 0.8728 (tpp) cc_final: 0.8452 (tpp) REVERT: B 603 ASP cc_start: 0.8273 (m-30) cc_final: 0.8028 (m-30) outliers start: 12 outliers final: 7 residues processed: 130 average time/residue: 0.2233 time to fit residues: 40.1122 Evaluate side-chains 126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 97 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1006 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= 0.215 Angle : 0.507 7.669 11852 Z= 0.253 Chirality : 0.040 0.233 1414 Planarity : 0.003 0.030 1454 Dihedral : 5.271 69.452 1178 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.58 % Allowed : 9.24 % 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 (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: 2.34 (0.26), residues: 1090 helix: 2.55 (0.19), residues: 734 sheet: 0.89 (0.65), residues: 70 loop : -1.05 (0.37), residues: 286 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 226 ARG 0.002 0.000 ARG B 472 *********************** 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: 15 poor density : 114 time to evaluate : 1.010 Fit side-chains REVERT: A 248 SER cc_start: 0.8242 (m) cc_final: 0.7913 (m) REVERT: A 457 ASN cc_start: 0.8524 (m-40) cc_final: 0.8074 (m-40) REVERT: A 584 ASN cc_start: 0.7068 (t0) cc_final: 0.6758 (t0) REVERT: B 166 LYS cc_start: 0.7186 (tttm) cc_final: 0.6730 (mtpp) REVERT: B 208 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7400 (mt) REVERT: B 244 MET cc_start: 0.8009 (mmm) cc_final: 0.7730 (mmm) REVERT: B 589 MET cc_start: 0.8717 (tpp) cc_final: 0.8422 (tpp) REVERT: B 603 ASP cc_start: 0.8296 (m-30) cc_final: 0.8064 (m-30) REVERT: B 604 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7935 (p90) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 0.2202 time to fit residues: 37.8774 Evaluate side-chains 126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** B 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1076 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= 0.181 Angle : 0.491 8.068 11852 Z= 0.245 Chirality : 0.040 0.235 1414 Planarity : 0.002 0.029 1454 Dihedral : 5.197 65.375 1178 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.00 % Allowed : 10.50 % Favored : 87.50 % 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 (0.26), residues: 1090 helix: 2.63 (0.19), residues: 734 sheet: 0.83 (0.65), residues: 70 loop : -1.09 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 409 HIS 0.003 0.001 HIS A 207 PHE 0.011 0.001 PHE A 217 TYR 0.010 0.001 TYR A 226 ARG 0.002 0.000 ARG B 472 *********************** 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 137 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.977 Fit side-chains REVERT: A 155 MET cc_start: 0.6281 (tpt) cc_final: 0.5278 (mtm) REVERT: A 457 ASN cc_start: 0.8500 (m-40) cc_final: 0.8048 (m-40) REVERT: A 584 ASN cc_start: 0.6972 (t0) cc_final: 0.6718 (t0) REVERT: B 166 LYS cc_start: 0.7184 (tttm) cc_final: 0.6743 (mtpp) REVERT: B 208 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7434 (mt) REVERT: B 244 MET cc_start: 0.7995 (mmm) cc_final: 0.7685 (mmm) REVERT: B 589 MET cc_start: 0.8710 (tpp) cc_final: 0.8413 (tpp) REVERT: B 603 ASP cc_start: 0.8292 (m-30) cc_final: 0.8050 (m-30) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.2114 time to fit residues: 38.7038 Evaluate side-chains 128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 710 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 54 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8792 Z= 0.252 Angle : 0.526 8.642 11852 Z= 0.263 Chirality : 0.041 0.230 1414 Planarity : 0.003 0.029 1454 Dihedral : 5.270 67.754 1178 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.21 % Allowed : 10.50 % Favored : 87.29 % 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: 2.24 (0.26), residues: 1090 helix: 2.55 (0.19), residues: 734 sheet: 1.28 (0.77), residues: 50 loop : -1.27 (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 0.021 0.001 PHE B 604 TYR 0.011 0.002 TYR A 226 ARG 0.004 0.000 ARG B 269 *********************** 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 135 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.908 Fit side-chains REVERT: A 248 SER cc_start: 0.8264 (m) cc_final: 0.7943 (m) REVERT: A 457 ASN cc_start: 0.8513 (m-40) cc_final: 0.8042 (m-40) REVERT: A 584 ASN cc_start: 0.7064 (t0) cc_final: 0.6799 (t0) REVERT: B 166 LYS cc_start: 0.7183 (tttm) cc_final: 0.6743 (mtpp) REVERT: B 208 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7410 (mt) REVERT: B 244 MET cc_start: 0.8079 (mmm) cc_final: 0.7683 (mmm) REVERT: B 603 ASP cc_start: 0.8284 (m-30) cc_final: 0.8052 (m-30) outliers start: 21 outliers final: 14 residues processed: 128 average time/residue: 0.2278 time to fit residues: 39.9815 Evaluate side-chains 128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 710 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 64 optimal weight: 0.4980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8792 Z= 0.152 Angle : 0.486 8.158 11852 Z= 0.243 Chirality : 0.039 0.208 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.168 61.188 1178 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.79 % Allowed : 11.13 % 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 (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: 2.34 (0.26), residues: 1090 helix: 2.61 (0.19), residues: 746 sheet: 1.29 (0.78), residues: 50 loop : -1.33 (0.35), residues: 294 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 0.027 0.001 PHE B 604 TYR 0.010 0.001 TYR B 179 ARG 0.001 0.000 ARG B 472 *********************** 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 133 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.894 Fit side-chains REVERT: A 155 MET cc_start: 0.6226 (tpt) cc_final: 0.5230 (mtm) REVERT: A 248 SER cc_start: 0.8169 (m) cc_final: 0.7843 (m) REVERT: A 457 ASN cc_start: 0.8488 (m-40) cc_final: 0.8033 (m-40) REVERT: A 584 ASN cc_start: 0.6962 (t0) cc_final: 0.6720 (t0) REVERT: A 604 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7815 (p90) REVERT: B 166 LYS cc_start: 0.7121 (tttm) cc_final: 0.6669 (mtpp) REVERT: B 208 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7417 (mt) REVERT: B 244 MET cc_start: 0.8001 (mmm) cc_final: 0.7664 (mmm) REVERT: B 589 MET cc_start: 0.8675 (tpp) cc_final: 0.8411 (tpp) REVERT: B 603 ASP cc_start: 0.8230 (m-30) cc_final: 0.7991 (m-30) outliers start: 17 outliers final: 15 residues processed: 125 average time/residue: 0.2165 time to fit residues: 37.2601 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 : 0.973 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8792 Z= 0.232 Angle : 0.516 7.958 11852 Z= 0.258 Chirality : 0.040 0.147 1414 Planarity : 0.003 0.029 1454 Dihedral : 5.221 64.184 1178 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.10 % Allowed : 11.45 % 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: 2.31 (0.26), residues: 1090 helix: 2.63 (0.19), residues: 734 sheet: 1.28 (0.78), residues: 50 loop : -1.32 (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 0.025 0.001 PHE B 604 TYR 0.011 0.001 TYR A 226 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 131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.011 Fit side-chains REVERT: A 155 MET cc_start: 0.6243 (tpt) cc_final: 0.5240 (mtm) REVERT: A 248 SER cc_start: 0.8244 (m) cc_final: 0.7909 (m) REVERT: A 457 ASN cc_start: 0.8523 (m-40) cc_final: 0.8051 (m-40) REVERT: A 584 ASN cc_start: 0.7059 (t0) cc_final: 0.6120 (p0) REVERT: A 604 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7809 (p90) REVERT: B 166 LYS cc_start: 0.7187 (tttm) cc_final: 0.6732 (mtpp) REVERT: B 208 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7396 (mt) REVERT: B 244 MET cc_start: 0.8068 (mmm) cc_final: 0.7655 (mmm) REVERT: B 603 ASP cc_start: 0.8252 (m-30) cc_final: 0.8012 (m-30) outliers start: 20 outliers final: 17 residues processed: 124 average time/residue: 0.2250 time to fit residues: 38.4223 Evaluate side-chains 129 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 587 VAL 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 710 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1247 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= 0.180 Angle : 0.497 6.241 11852 Z= 0.249 Chirality : 0.039 0.144 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.208 63.008 1178 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.10 % Allowed : 11.55 % 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: 2.27 (0.26), residues: 1090 helix: 2.56 (0.19), residues: 746 sheet: 1.28 (0.78), residues: 50 loop : -1.40 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 409 HIS 0.002 0.001 HIS A 249 PHE 0.024 0.001 PHE B 604 TYR 0.010 0.001 TYR A 226 ARG 0.001 0.000 ARG B 494 *********************** 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 132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.960 Fit side-chains REVERT: A 155 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5245 (mtm) REVERT: A 248 SER cc_start: 0.8211 (m) cc_final: 0.7876 (m) REVERT: A 457 ASN cc_start: 0.8522 (m-40) cc_final: 0.8049 (m-40) REVERT: A 584 ASN cc_start: 0.7030 (t0) cc_final: 0.6121 (p0) REVERT: A 604 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7791 (p90) REVERT: B 166 LYS cc_start: 0.7167 (tttm) cc_final: 0.6719 (mtpp) REVERT: B 208 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7386 (mt) REVERT: B 244 MET cc_start: 0.8025 (mmm) cc_final: 0.7608 (mmm) REVERT: B 560 LYS cc_start: 0.8662 (mttt) cc_final: 0.7817 (mtpp) REVERT: B 603 ASP cc_start: 0.8243 (m-30) cc_final: 0.8002 (m-30) outliers start: 20 outliers final: 17 residues processed: 124 average time/residue: 0.2368 time to fit residues: 40.1477 Evaluate side-chains 131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET 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 587 VAL 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 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8792 Z= 0.207 Angle : 0.511 8.005 11852 Z= 0.255 Chirality : 0.040 0.166 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.224 63.670 1178 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 (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: 2.23 (0.26), residues: 1090 helix: 2.53 (0.19), residues: 746 sheet: 1.25 (0.78), residues: 50 loop : -1.39 (0.35), residues: 294 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 0.024 0.001 PHE B 604 TYR 0.010 0.001 TYR A 226 ARG 0.002 0.000 ARG A 498 ********************** 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 129 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.983 Fit side-chains REVERT: A 155 MET cc_start: 0.6269 (tpt) cc_final: 0.5259 (mtm) REVERT: A 248 SER cc_start: 0.8225 (m) cc_final: 0.7892 (m) REVERT: A 457 ASN cc_start: 0.8526 (m-40) cc_final: 0.8199 (m110) REVERT: A 584 ASN cc_start: 0.7071 (t0) cc_final: 0.6160 (p0) REVERT: A 604 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7848 (p90) REVERT: B 166 LYS cc_start: 0.7178 (tttm) cc_final: 0.6729 (mtpp) REVERT: B 208 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7395 (mt) REVERT: B 244 MET cc_start: 0.8063 (mmm) cc_final: 0.7640 (mmm) REVERT: B 560 LYS cc_start: 0.8681 (mttt) cc_final: 0.7831 (mtpp) REVERT: B 603 ASP cc_start: 0.8252 (m-30) cc_final: 0.8013 (m-30) outliers start: 19 outliers final: 16 residues processed: 122 average time/residue: 0.2206 time to fit residues: 37.4715 Evaluate side-chains 128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 587 VAL Chi-restraints excluded: chain A residue 604 PHE 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 710 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.143953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115878 restraints weight = 9952.613| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.72 r_work: 0.3060 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8792 Z= 0.185 Angle : 0.501 6.460 11852 Z= 0.250 Chirality : 0.040 0.136 1414 Planarity : 0.002 0.028 1454 Dihedral : 5.222 61.242 1178 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.00 % Allowed : 11.97 % 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: 2.29 (0.26), residues: 1090 helix: 2.57 (0.19), residues: 746 sheet: 1.25 (0.79), residues: 50 loop : -1.35 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 409 HIS 0.003 0.001 HIS A 249 PHE 0.023 0.001 PHE B 604 TYR 0.010 0.001 TYR A 225 ARG 0.001 0.000 ARG B 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.37 seconds wall clock time: 43 minutes 26.96 seconds (2606.96 seconds total)