Starting phenix.real_space_refine on Thu Mar 13 12:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vow_43393/03_2025/8vow_43393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vow_43393/03_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_43393/03_2025/8vow_43393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vow_43393/03_2025/8vow_43393.map" model { file = "/net/cci-nas-00/data/ceres_data/8vow_43393/03_2025/8vow_43393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vow_43393/03_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-5624/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: 6.65, per 1000 atoms: 0.75 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 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: 0.96 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: 2.68 Time building geometry restraints manager: 2.92 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: 2.940 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: 0.060 Set scattering table: 0.070 Process input model: 24.750 Find NCS groups from input model: 0.390 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- 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 : 0.995 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: 0.1920 time to fit residues: 45.3385 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 : 1.020 ------------------------------------------------------------------------------- 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 = 0.151979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127674 restraints weight = 12044.827| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.81 r_work: 0.3441 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1048 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 9.143 12222 Z= 0.288 Chirality : 0.040 0.157 1460 Planarity : 0.003 0.035 1504 Dihedral : 7.773 67.605 1238 Min Nonbonded Distance : 1.832 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: 2.34 (0.19), residues: 738 sheet: -1.12 (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 : 0.965 Fit side-chains REVERT: A 627 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7641 (mm-40) REVERT: A 718 TRP cc_start: 0.8206 (t-100) cc_final: 0.7949 (t-100) REVERT: B 554 SER cc_start: 0.8454 (p) cc_final: 0.8108 (p) outliers start: 18 outliers final: 13 residues processed: 137 average time/residue: 0.1895 time to fit residues: 38.0995 Evaluate side-chains 130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 0.3980 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 102 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 679 HIS ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131271 restraints weight = 11986.449| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.81 r_work: 0.3492 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9054 Z= 0.149 Angle : 0.514 9.080 12222 Z= 0.261 Chirality : 0.038 0.143 1460 Planarity : 0.003 0.037 1504 Dihedral : 7.506 65.310 1238 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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: 1.52 (0.26), residues: 1127 helix: 2.57 (0.19), residues: 738 sheet: -1.19 (0.70), residues: 35 loop : -2.37 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 718 HIS 0.002 0.001 HIS A 602 PHE 0.018 0.001 PHE B 435 TYR 0.015 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 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.054 Fit side-chains REVERT: A 687 LEU cc_start: 0.6478 (mm) cc_final: 0.6270 (mm) REVERT: B 353 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7734 (tptt) outliers start: 11 outliers final: 7 residues processed: 140 average time/residue: 0.1875 time to fit residues: 38.1810 Evaluate side-chains 130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 679 HIS 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: 0.5980 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN A 679 HIS ** 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 = 0.3859 r_free = 0.3859 target = 0.155234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131262 restraints weight = 12088.642| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.83 r_work: 0.3489 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1257 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= 0.164 Angle : 0.511 9.193 12222 Z= 0.258 Chirality : 0.038 0.139 1460 Planarity : 0.003 0.037 1504 Dihedral : 7.439 64.911 1238 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.34 % Allowed : 14.08 % Favored : 84.58 % 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: 1.54 (0.26), residues: 1127 helix: 2.57 (0.19), residues: 741 sheet: -1.28 (0.68), residues: 35 loop : -2.35 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 718 HIS 0.010 0.001 HIS A 679 PHE 0.015 0.001 PHE B 217 TYR 0.013 0.001 TYR B 495 ARG 0.002 0.000 ARG B 277 *********************** 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 142 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.083 Fit side-chains REVERT: A 680 ARG cc_start: 0.7998 (tpt170) cc_final: 0.7775 (tpt170) REVERT: B 277 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7441 (tpt-90) REVERT: B 353 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7754 (tptt) outliers start: 13 outliers final: 9 residues processed: 138 average time/residue: 0.1991 time to fit residues: 40.3849 Evaluate side-chains 132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 324 THR Chi-restraints excluded: chain A residue 679 HIS 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 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: 0.9980 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.155088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.131113 restraints weight = 11986.953| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.81 r_work: 0.3489 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1333 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= 0.169 Angle : 0.509 9.236 12222 Z= 0.256 Chirality : 0.039 0.139 1460 Planarity : 0.003 0.037 1504 Dihedral : 7.383 64.402 1238 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.54 % Allowed : 15.01 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1127 helix: 2.59 (0.19), residues: 741 sheet: -1.18 (0.70), residues: 35 loop : -2.37 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 718 HIS 0.013 0.001 HIS A 679 PHE 0.015 0.001 PHE B 217 TYR 0.013 0.001 TYR B 495 ARG 0.002 0.000 ARG B 680 *********************** 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 143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.939 Fit side-chains REVERT: B 353 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7707 (tptt) outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.1923 time to fit residues: 38.9991 Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL 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 604 PHE Chi-restraints excluded: chain B residue 699 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 9 optimal weight: 0.0170 chunk 109 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9822 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.154070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130006 restraints weight = 12022.997| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.83 r_work: 0.3473 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1438 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 : 0.531 9.212 12222 Z= 0.265 Chirality : 0.039 0.140 1460 Planarity : 0.003 0.035 1504 Dihedral : 7.361 64.089 1238 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.85 % Allowed : 15.31 % Favored : 82.84 % 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: 1.51 (0.26), residues: 1127 helix: 2.55 (0.19), residues: 741 sheet: -1.18 (0.69), residues: 35 loop : -2.38 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 718 HIS 0.003 0.001 HIS A 249 PHE 0.016 0.001 PHE A 715 TYR 0.014 0.001 TYR B 495 ARG 0.002 0.000 ARG A 680 *********************** 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 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.882 Fit side-chains REVERT: A 495 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.6811 (t80) REVERT: A 687 LEU cc_start: 0.6415 (mm) cc_final: 0.6025 (mm) REVERT: B 353 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7761 (tptt) outliers start: 18 outliers final: 13 residues processed: 134 average time/residue: 0.1826 time to fit residues: 35.3938 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 109 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** 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 = 0.3851 r_free = 0.3851 target = 0.154602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130397 restraints weight = 12161.060| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.83 r_work: 0.3481 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1495 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= 0.175 Angle : 0.526 9.282 12222 Z= 0.262 Chirality : 0.039 0.146 1460 Planarity : 0.003 0.034 1504 Dihedral : 7.298 63.470 1238 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.85 % Allowed : 15.93 % Favored : 82.22 % 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: 2.60 (0.19), residues: 734 sheet: -1.08 (0.71), residues: 35 loop : -2.31 (0.30), residues: 358 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 0.022 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 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.941 Fit side-chains REVERT: A 495 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.6883 (t80) REVERT: A 627 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7521 (mm-40) REVERT: A 687 LEU cc_start: 0.6500 (mm) cc_final: 0.6045 (mm) REVERT: B 353 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7748 (tptt) outliers start: 18 outliers final: 13 residues processed: 135 average time/residue: 0.1889 time to fit residues: 37.5994 Evaluate side-chains 132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL 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 534 ASN 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: 0.4980 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 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 414 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 = 0.3850 r_free = 0.3850 target = 0.154506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130315 restraints weight = 12268.662| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.84 r_work: 0.3480 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1552 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= 0.177 Angle : 0.526 9.242 12222 Z= 0.263 Chirality : 0.039 0.182 1460 Planarity : 0.003 0.034 1504 Dihedral : 7.256 63.113 1238 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % 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: 1.57 (0.26), residues: 1127 helix: 2.60 (0.19), residues: 734 sheet: -0.99 (0.71), residues: 35 loop : -2.28 (0.30), residues: 358 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 0.021 0.001 PHE A 604 TYR 0.013 0.001 TYR B 225 ARG 0.002 0.000 ARG A 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 138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.924 Fit side-chains REVERT: A 285 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7492 (tt) REVERT: A 495 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.6962 (t80) REVERT: A 627 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: B 353 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7750 (tptt) outliers start: 17 outliers final: 11 residues processed: 134 average time/residue: 0.1808 time to fit residues: 35.6574 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 : 0.902 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 75 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 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131037 restraints weight = 12035.647| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.80 r_work: 0.3483 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1575 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 : 0.541 9.933 12222 Z= 0.267 Chirality : 0.039 0.178 1460 Planarity : 0.003 0.034 1504 Dihedral : 7.219 62.742 1238 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.44 % Allowed : 16.75 % Favored : 81.81 % 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: 2.57 (0.19), residues: 736 sheet: -0.93 (0.72), residues: 35 loop : -2.29 (0.30), residues: 356 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 0.021 0.001 PHE A 604 TYR 0.013 0.001 TYR B 225 ARG 0.003 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 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.923 Fit side-chains REVERT: A 285 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7473 (tt) REVERT: A 495 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.6969 (t80) REVERT: A 687 LEU cc_start: 0.6389 (mm) cc_final: 0.6019 (mm) REVERT: B 353 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7750 (tptt) outliers start: 14 outliers final: 12 residues processed: 133 average time/residue: 0.1835 time to fit residues: 36.2039 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 : 1.050 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.155758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.131734 restraints weight = 12118.300| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.82 r_work: 0.3499 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1662 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= 0.167 Angle : 0.534 9.917 12222 Z= 0.264 Chirality : 0.039 0.164 1460 Planarity : 0.003 0.037 1504 Dihedral : 7.112 61.782 1238 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: 1.60 (0.26), residues: 1127 helix: 2.62 (0.19), residues: 734 sheet: -0.77 (0.73), residues: 35 loop : -2.30 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 718 HIS 0.002 0.001 HIS A 249 PHE 0.022 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 138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.030 Fit side-chains REVERT: A 285 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7472 (tt) REVERT: A 495 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7067 (t80) REVERT: A 687 LEU cc_start: 0.6417 (mm) cc_final: 0.6100 (mm) REVERT: B 353 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7744 (tptt) REVERT: B 464 GLU cc_start: 0.7840 (tp30) cc_final: 0.7346 (tp30) outliers start: 15 outliers final: 13 residues processed: 135 average time/residue: 0.1793 time to fit residues: 35.6719 Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 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 67 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.0670 chunk 26 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.131627 restraints weight = 12188.515| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.83 r_work: 0.3494 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 9054 Z= 0.257 Angle : 0.887 59.184 12222 Z= 0.522 Chirality : 0.039 0.183 1460 Planarity : 0.003 0.040 1504 Dihedral : 7.138 61.786 1238 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.54 % Allowed : 17.27 % Favored : 81.19 % Cbeta Deviations : 0.09 % 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: 1.54 (0.26), residues: 1127 helix: 2.56 (0.19), residues: 734 sheet: -0.76 (0.73), residues: 35 loop : -2.31 (0.30), residues: 358 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 715 TYR 0.013 0.001 TYR B 225 ARG 0.003 0.000 ARG B 277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4282.18 seconds wall clock time: 75 minutes 3.37 seconds (4503.37 seconds total)