Starting phenix.real_space_refine on Thu Jan 16 00:03:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vow_43393/01_2025/8vow_43393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vow_43393/01_2025/8vow_43393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vow_43393/01_2025/8vow_43393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vow_43393/01_2025/8vow_43393.map" model { file = "/net/cci-nas-00/data/ceres_data/8vow_43393/01_2025/8vow_43393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vow_43393/01_2025/8vow_43393.cif" } resolution = 3.44 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= 0.003 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 5 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 5776 2.51 5 N 1444 2.21 5 O 1659 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-5571/modules/chem_data/mon_lib" Total number of atoms: 8917 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4430 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 10, 'TRANS': 555} Chain: "B" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4422 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 10, 'TRANS': 554} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.41, per 1000 atoms: 0.72 Number of scatterers: 8917 At special positions: 0 Unit cell: (70.523, 97.05, 140.399, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 30 16.00 P 5 15.00 Mg 2 11.99 O 1659 8.00 N 1444 7.00 C 5776 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: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 5 sheets defined 70.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.539A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.587A pdb=" N LEU A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 251 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.897A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 272 removed outlier: 3.700A pdb=" N ILE A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.842A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 305 removed outlier: 4.668A pdb=" N VAL A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY A 297 " --> pdb=" O MET A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 326 Processing helix chain 'A' and resid 327 through 354 removed outlier: 3.736A pdb=" N GLN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 363 through 417 removed outlier: 3.627A pdb=" N LEU A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.819A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) 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 464 Proline residue: A 447 - end of helix Processing helix chain 'A' and resid 524 through 533 removed outlier: 3.542A pdb=" N ALA A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.624A pdb=" N GLY A 547 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.703A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 607 removed outlier: 3.511A pdb=" N LYS A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.580A pdb=" N LEU A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 666 removed outlier: 3.622A pdb=" N TYR A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 710 removed outlier: 3.542A pdb=" N LEU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.957A pdb=" N GLN A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 721 " --> pdb=" O MET A 717 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 723 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 188 removed outlier: 4.005A pdb=" N PHE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 196 Processing helix chain 'B' and resid 202 through 251 removed outlier: 3.585A pdb=" N ILE B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.763A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.631A pdb=" N ILE B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 279 removed outlier: 3.898A pdb=" N ALA B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.680A pdb=" N MET B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 307 through 354 removed outlier: 4.364A pdb=" N ILE B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.972A 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 417 Processing helix chain 'B' and resid 421 through 432 removed outlier: 3.515A pdb=" N LEU B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 436 through 464 Proline residue: B 447 - end of helix removed outlier: 3.752A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.856A pdb=" N ARG B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 498 removed outlier: 3.855A pdb=" N LEU B 497 " --> pdb=" O ARG B 494 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 498 " --> pdb=" O TYR B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 494 through 498' 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 562 Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.731A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 624 through 639 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 684 removed outlier: 3.501A pdb=" N THR B 683 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 Processing helix chain 'B' and resid 712 through 722 Processing sheet with id=AA1, first strand: chain 'A' and resid 502 through 505 removed outlier: 3.526A pdb=" N PHE A 493 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 491 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 489 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 542 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 491 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS A 540 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 562 through 565 removed outlier: 6.759A pdb=" N ALA A 563 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASP A 647 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL A 565 " --> pdb=" O ASP A 647 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 515 " --> pdb=" O ILE A 676 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 693 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 502 through 509 removed outlier: 6.254A pdb=" N LYS B 503 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASP B 492 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE B 505 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 490 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 645 through 647 removed outlier: 8.994A pdb=" N TYR B 691 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA B 516 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU B 693 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 518 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU B 700 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS B 694 " --> pdb=" O ILE B 698 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 574 through 575 573 hydrogen bonds defined for protein. 1683 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: 2.32 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2825 1.36 - 1.50: 2155 1.50 - 1.63: 4010 1.63 - 1.77: 0 1.77 - 1.91: 64 Bond restraints: 9054 Sorted by residual: bond pdb=" CA TYR A 691 " pdb=" CB TYR A 691 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.38e-02 5.25e+03 3.74e+00 bond pdb=" C TYR A 691 " pdb=" O TYR A 691 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.19e-02 7.06e+03 1.77e+00 bond pdb=" C ARG A 494 " pdb=" N TYR A 495 " ideal model delta sigma weight residual 1.332 1.314 0.018 1.40e-02 5.10e+03 1.67e+00 bond pdb=" C ASP A 671 " pdb=" N VAL A 672 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.05e-02 9.07e+03 1.63e+00 bond pdb=" CA ASP A 671 " pdb=" C ASP A 671 " ideal model delta sigma weight residual 1.526 1.507 0.019 1.51e-02 4.39e+03 1.53e+00 ... (remaining 9049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11997 1.69 - 3.38: 176 3.38 - 5.07: 34 5.07 - 6.76: 13 6.76 - 8.45: 2 Bond angle restraints: 12222 Sorted by residual: angle pdb=" O ASP A 670 " pdb=" C ASP A 670 " pdb=" N ASP A 671 " ideal model delta sigma weight residual 122.19 124.83 -2.64 1.03e+00 9.43e-01 6.54e+00 angle pdb=" N GLN B 446 " pdb=" CA GLN B 446 " pdb=" C GLN B 446 " ideal model delta sigma weight residual 109.81 115.16 -5.35 2.21e+00 2.05e-01 5.87e+00 angle pdb=" CA LEU B 610 " pdb=" CB LEU B 610 " pdb=" CG LEU B 610 " ideal model delta sigma weight residual 116.30 124.75 -8.45 3.50e+00 8.16e-02 5.83e+00 angle pdb=" C ARG A 680 " pdb=" N LEU A 681 " pdb=" CA LEU A 681 " ideal model delta sigma weight residual 121.54 125.87 -4.33 1.91e+00 2.74e-01 5.13e+00 angle pdb=" O2B ADP B 801 " pdb=" PB ADP B 801 " pdb=" O3B ADP B 801 " ideal model delta sigma weight residual 119.90 113.17 6.73 3.00e+00 1.11e-01 5.04e+00 ... (remaining 12217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4871 17.94 - 35.88: 499 35.88 - 53.81: 89 53.81 - 71.75: 20 71.75 - 89.69: 9 Dihedral angle restraints: 5488 sinusoidal: 2215 harmonic: 3273 Sorted by residual: dihedral pdb=" CA LEU A 497 " pdb=" C LEU A 497 " pdb=" N ARG A 498 " pdb=" CA ARG A 498 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ARG B 269 " pdb=" C ARG B 269 " pdb=" N PHE B 270 " pdb=" CA PHE B 270 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU A 606 " pdb=" CG GLU A 606 " pdb=" CD GLU A 606 " pdb=" OE1 GLU A 606 " ideal model delta sinusoidal sigma weight residual 0.00 -89.69 89.69 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 969 0.032 - 0.063: 327 0.063 - 0.094: 109 0.094 - 0.126: 47 0.126 - 0.157: 8 Chirality restraints: 1460 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 2.80 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ILE B 509 " pdb=" N ILE B 509 " pdb=" C ILE B 509 " pdb=" CB ILE B 509 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE B 690 " pdb=" N ILE B 690 " pdb=" C ILE B 690 " pdb=" CB ILE B 690 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1457 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 446 " 0.025 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 447 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 447 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 447 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 684 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.86e+00 pdb=" C ILE B 684 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE B 684 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 685 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 508 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C THR B 508 " 0.020 2.00e-02 2.50e+03 pdb=" O THR B 508 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE B 509 " -0.007 2.00e-02 2.50e+03 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 53 2.51 - 3.11: 6793 3.11 - 3.71: 13810 3.71 - 4.30: 18731 4.30 - 4.90: 32226 Nonbonded interactions: 71613 Sorted by model distance: nonbonded pdb=" O2B ADP B 801 " pdb="MG MG B 803 " model vdw 1.916 2.170 nonbonded pdb=" O4 VO4 B 802 " pdb="MG MG B 803 " model vdw 1.923 2.170 nonbonded pdb=" O1 VO4 B 802 " pdb="MG MG B 803 " model vdw 1.924 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.999 2.170 nonbonded pdb=" O3B ATP A 801 " pdb="MG MG A 802 " model vdw 2.049 2.170 ... (remaining 71608 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' and (resid 158 through 722 or resid 802)) selection = (chain 'B' and (resid 158 through 722 or resid 803)) } 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: 3.330 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.730 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 9054 Z= 0.172 Angle : 0.555 8.451 12222 Z= 0.280 Chirality : 0.039 0.157 1460 Planarity : 0.003 0.037 1504 Dihedral : 15.065 89.689 3378 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.21 % Allowed : 0.10 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1127 helix: 2.36 (0.20), residues: 725 sheet: -0.77 (0.77), residues: 35 loop : -2.19 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 409 HIS 0.003 0.001 HIS A 679 PHE 0.018 0.001 PHE A 715 TYR 0.017 0.001 TYR B 495 ARG 0.003 0.000 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.972 Fit side-chains REVERT: A 680 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7555 (tpt170) REVERT: B 302 TYR cc_start: 0.8084 (t80) cc_final: 0.7785 (t80) REVERT: B 554 SER cc_start: 0.8319 (p) cc_final: 0.8010 (p) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.1858 time to fit residues: 43.3707 Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN A 627 GLN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.152016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127733 restraints weight = 12040.160| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.81 r_work: 0.3432 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9054 Z= 0.255 Angle : 0.572 9.150 12222 Z= 0.288 Chirality : 0.040 0.155 1460 Planarity : 0.003 0.035 1504 Dihedral : 7.775 67.647 1238 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.85 % Allowed : 10.48 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1127 helix: 2.33 (0.19), residues: 738 sheet: -1.13 (0.71), residues: 35 loop : -2.48 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 718 HIS 0.004 0.001 HIS B 679 PHE 0.035 0.002 PHE B 435 TYR 0.017 0.001 TYR B 495 ARG 0.005 0.000 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.930 Fit side-chains REVERT: A 627 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7641 (mm-40) REVERT: A 718 TRP cc_start: 0.8203 (t-100) cc_final: 0.7948 (t-100) REVERT: B 554 SER cc_start: 0.8448 (p) cc_final: 0.8103 (p) outliers start: 18 outliers final: 13 residues processed: 138 average time/residue: 0.1939 time to fit residues: 38.6338 Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 87 optimal weight: 0.0170 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 622 ASN A 627 GLN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130063 restraints weight = 12022.466| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.81 r_work: 0.3473 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9054 Z= 0.167 Angle : 0.520 9.032 12222 Z= 0.264 Chirality : 0.039 0.144 1460 Planarity : 0.003 0.037 1504 Dihedral : 7.544 65.587 1238 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.13 % Allowed : 12.74 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1127 helix: 2.51 (0.19), residues: 739 sheet: -1.19 (0.70), residues: 35 loop : -2.36 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 PHE 0.018 0.001 PHE B 435 TYR 0.017 0.001 TYR B 495 ARG 0.003 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.055 Fit side-chains REVERT: A 285 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7616 (tt) REVERT: B 353 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7746 (tptt) outliers start: 11 outliers final: 7 residues processed: 136 average time/residue: 0.1943 time to fit residues: 38.1083 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 431 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN ** A 720 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 = 0.3853 r_free = 0.3853 target = 0.154809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130869 restraints weight = 12096.469| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.83 r_work: 0.3484 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9054 Z= 0.161 Angle : 0.508 9.236 12222 Z= 0.256 Chirality : 0.039 0.140 1460 Planarity : 0.003 0.037 1504 Dihedral : 7.412 64.604 1238 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.85 % Allowed : 14.08 % Favored : 84.07 % 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: 1.56 (0.26), residues: 1127 helix: 2.59 (0.19), residues: 742 sheet: -1.16 (0.70), residues: 35 loop : -2.40 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 PHE 0.016 0.001 PHE A 604 TYR 0.014 0.001 TYR B 495 ARG 0.002 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.028 Fit side-chains REVERT: A 285 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7606 (tt) REVERT: B 353 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7713 (tptt) REVERT: B 700 GLU cc_start: 0.8323 (pm20) cc_final: 0.7957 (pm20) outliers start: 18 outliers final: 11 residues processed: 148 average time/residue: 0.1976 time to fit residues: 41.8006 Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 627 GLN A 720 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.154689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130738 restraints weight = 12005.899| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.82 r_work: 0.3479 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9054 Z= 0.165 Angle : 0.509 9.231 12222 Z= 0.258 Chirality : 0.039 0.139 1460 Planarity : 0.003 0.036 1504 Dihedral : 7.333 63.953 1238 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.16 % Allowed : 14.90 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1127 helix: 2.59 (0.19), residues: 741 sheet: -1.16 (0.69), residues: 35 loop : -2.40 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 PHE 0.015 0.001 PHE B 217 TYR 0.012 0.001 TYR B 225 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.017 Fit side-chains REVERT: A 285 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7591 (tt) REVERT: A 495 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.6705 (t80) REVERT: A 687 LEU cc_start: 0.6340 (mm) cc_final: 0.6060 (mm) REVERT: B 353 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7744 (tptt) REVERT: B 700 GLU cc_start: 0.8336 (pm20) cc_final: 0.7958 (pm20) outliers start: 21 outliers final: 13 residues processed: 147 average time/residue: 0.1916 time to fit residues: 40.6299 Evaluate side-chains 140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 9 optimal weight: 0.0170 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN A 659 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130962 restraints weight = 11914.076| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.80 r_work: 0.3491 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9054 Z= 0.168 Angle : 0.525 9.317 12222 Z= 0.261 Chirality : 0.039 0.139 1460 Planarity : 0.003 0.035 1504 Dihedral : 7.279 63.434 1238 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.95 % Allowed : 15.62 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1127 helix: 2.63 (0.19), residues: 739 sheet: -1.01 (0.71), residues: 35 loop : -2.38 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 PHE 0.016 0.001 PHE A 604 TYR 0.012 0.001 TYR B 225 ARG 0.002 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.999 Fit side-chains REVERT: A 285 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7585 (tt) REVERT: A 495 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.6747 (t80) REVERT: A 627 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7631 (mm-40) REVERT: A 659 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.7099 (t0) REVERT: A 687 LEU cc_start: 0.6487 (mm) cc_final: 0.6183 (mm) REVERT: B 353 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7742 (tptt) REVERT: B 700 GLU cc_start: 0.8379 (pm20) cc_final: 0.7976 (pm20) outliers start: 19 outliers final: 12 residues processed: 137 average time/residue: 0.1914 time to fit residues: 38.2658 Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN ** A 659 ASN ** 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 = 0.3831 r_free = 0.3831 target = 0.152913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128538 restraints weight = 12236.348| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.83 r_work: 0.3448 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9054 Z= 0.229 Angle : 0.536 9.198 12222 Z= 0.269 Chirality : 0.040 0.161 1460 Planarity : 0.003 0.033 1504 Dihedral : 7.347 63.904 1238 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.85 % Allowed : 15.62 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1127 helix: 2.54 (0.19), residues: 735 sheet: -1.00 (0.70), residues: 35 loop : -2.38 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 409 HIS 0.003 0.001 HIS A 249 PHE 0.023 0.001 PHE A 604 TYR 0.013 0.001 TYR B 495 ARG 0.002 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.111 Fit side-chains REVERT: A 236 MET cc_start: 0.7467 (ttp) cc_final: 0.7189 (tpp) REVERT: A 285 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7624 (tt) REVERT: A 495 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.6938 (t80) REVERT: A 627 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7685 (mm-40) REVERT: B 353 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7815 (tptt) REVERT: B 464 GLU cc_start: 0.7892 (tp30) cc_final: 0.7677 (tp30) REVERT: B 700 GLU cc_start: 0.8469 (pm20) cc_final: 0.8076 (pm20) outliers start: 18 outliers final: 11 residues processed: 137 average time/residue: 0.1898 time to fit residues: 37.6573 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129854 restraints weight = 12311.129| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.83 r_work: 0.3467 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9054 Z= 0.178 Angle : 0.535 9.316 12222 Z= 0.265 Chirality : 0.039 0.170 1460 Planarity : 0.003 0.034 1504 Dihedral : 7.245 63.078 1238 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.75 % Allowed : 16.14 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1127 helix: 2.59 (0.19), residues: 739 sheet: -0.96 (0.71), residues: 35 loop : -2.37 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 409 HIS 0.002 0.001 HIS A 249 PHE 0.017 0.001 PHE A 715 TYR 0.014 0.001 TYR B 495 ARG 0.002 0.000 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.979 Fit side-chains REVERT: A 285 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7619 (tt) REVERT: A 495 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.6908 (t80) REVERT: A 687 LEU cc_start: 0.6486 (mm) cc_final: 0.6168 (mm) REVERT: B 353 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7806 (tptt) REVERT: B 464 GLU cc_start: 0.7859 (tp30) cc_final: 0.7635 (tp30) REVERT: B 700 GLU cc_start: 0.8470 (pm20) cc_final: 0.8076 (pm20) outliers start: 17 outliers final: 12 residues processed: 137 average time/residue: 0.1838 time to fit residues: 36.7999 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.129823 restraints weight = 12115.654| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.82 r_work: 0.3469 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9054 Z= 0.190 Angle : 0.550 9.862 12222 Z= 0.272 Chirality : 0.039 0.204 1460 Planarity : 0.003 0.035 1504 Dihedral : 7.240 62.880 1238 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.75 % Allowed : 16.34 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1127 helix: 2.54 (0.19), residues: 734 sheet: -0.86 (0.72), residues: 35 loop : -2.35 (0.30), residues: 358 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 0.016 0.001 PHE B 217 TYR 0.013 0.001 TYR B 495 ARG 0.002 0.000 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.958 Fit side-chains REVERT: A 285 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7596 (tt) REVERT: A 495 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6936 (t80) REVERT: A 627 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7589 (mm-40) REVERT: A 687 LEU cc_start: 0.6519 (mm) cc_final: 0.6259 (mm) REVERT: B 353 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7775 (tptt) REVERT: B 464 GLU cc_start: 0.7889 (tp30) cc_final: 0.7660 (tp30) REVERT: B 700 GLU cc_start: 0.8471 (pm20) cc_final: 0.8056 (pm20) outliers start: 17 outliers final: 14 residues processed: 132 average time/residue: 0.1887 time to fit residues: 36.3695 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 GLN Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 110 optimal weight: 0.0000 chunk 79 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.155039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130965 restraints weight = 12133.353| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.82 r_work: 0.3484 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9054 Z= 0.166 Angle : 0.538 10.572 12222 Z= 0.268 Chirality : 0.039 0.191 1460 Planarity : 0.003 0.036 1504 Dihedral : 7.154 62.199 1238 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.44 % Allowed : 16.86 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1127 helix: 2.62 (0.19), residues: 734 sheet: -0.84 (0.73), residues: 35 loop : -2.30 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 PHE 0.021 0.001 PHE A 715 TYR 0.013 0.001 TYR B 225 ARG 0.002 0.000 ARG A 680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.931 Fit side-chains REVERT: A 285 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7579 (tt) REVERT: A 495 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7046 (t80) REVERT: A 687 LEU cc_start: 0.6556 (mm) cc_final: 0.6291 (mm) REVERT: B 196 ASP cc_start: 0.7607 (m-30) cc_final: 0.7315 (m-30) REVERT: B 353 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7774 (tptt) REVERT: B 464 GLU cc_start: 0.7871 (tp30) cc_final: 0.7642 (tp30) REVERT: B 700 GLU cc_start: 0.8517 (pm20) cc_final: 0.8098 (pm20) outliers start: 14 outliers final: 12 residues processed: 134 average time/residue: 0.1968 time to fit residues: 38.7158 Evaluate side-chains 132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 604 PHE Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.0470 chunk 26 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.156305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132363 restraints weight = 12159.436| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.83 r_work: 0.3499 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9054 Z= 0.159 Angle : 0.533 10.516 12222 Z= 0.264 Chirality : 0.039 0.188 1460 Planarity : 0.003 0.037 1504 Dihedral : 7.081 61.425 1238 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.54 % Allowed : 16.75 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1127 helix: 2.65 (0.19), residues: 734 sheet: -0.71 (0.74), residues: 35 loop : -2.29 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 409 HIS 0.002 0.001 HIS A 249 PHE 0.015 0.001 PHE B 217 TYR 0.013 0.001 TYR B 225 ARG 0.002 0.000 ARG B 680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4257.58 seconds wall clock time: 76 minutes 56.68 seconds (4616.68 seconds total)