Starting phenix.real_space_refine on Sun Apr 7 12:22:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/04_2024/8shc_40483_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/04_2024/8shc_40483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/04_2024/8shc_40483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/04_2024/8shc_40483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/04_2024/8shc_40483_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shc_40483/04_2024/8shc_40483_updated.pdb" } resolution = 3.0 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= 0.041 sd= 0.266 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 P 6 5.49 5 S 36 5.16 5 Cl 2 4.86 5 C 7056 2.51 5 N 1550 2.21 5 O 1802 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 259": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "C" Number of atoms: 4755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4755 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 24, 'TRANS': 588} Chain breaks: 3 Chain: "D" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 477 Unusual residues: {' CL': 1, 'AV0': 2, 'CLR': 6, 'LBN': 9, 'NFL': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 477 Unusual residues: {' CL': 1, 'AV0': 2, 'CLR': 6, 'LBN': 9, 'NFL': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 351 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'LBN:plan-2': 6, 'LBN:plan-3': 7, 'LBN:plan-1': 7} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 6.36, per 1000 atoms: 0.61 Number of scatterers: 10464 At special positions: 0 Unit cell: (122.1, 73.7, 107.8, 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) Cl 2 17.00 S 36 16.00 P 6 15.00 F 12 9.00 O 1802 8.00 N 1550 7.00 C 7056 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 4 sheets defined 63.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 80 through 105 removed outlier: 4.183A pdb=" N LEU D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 130 Proline residue: D 123 - end of helix removed outlier: 4.543A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 155 Processing helix chain 'D' and resid 158 through 161 No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 178 through 205 Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 217 through 240 Processing helix chain 'D' and resid 252 through 266 removed outlier: 5.374A pdb=" N GLY D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 291 Processing helix chain 'D' and resid 302 through 317 Processing helix chain 'D' and resid 319 through 322 No H-bonds generated for 'chain 'D' and resid 319 through 322' Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.945A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 375 removed outlier: 4.006A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 398 removed outlier: 3.539A pdb=" N PHE D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'D' and resid 422 through 436 Processing helix chain 'D' and resid 440 through 442 No H-bonds generated for 'chain 'D' and resid 440 through 442' Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.930A pdb=" N LEU D 458 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N MET D 461 " --> pdb=" O ASN D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 474 Proline residue: D 469 - end of helix Processing helix chain 'D' and resid 476 through 490 Processing helix chain 'D' and resid 494 through 514 Processing helix chain 'D' and resid 533 through 536 No H-bonds generated for 'chain 'D' and resid 533 through 536' Processing helix chain 'D' and resid 556 through 570 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 670 through 685 Processing helix chain 'D' and resid 697 through 705 Processing helix chain 'D' and resid 724 through 730 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 80 through 105 removed outlier: 4.183A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 Proline residue: C 123 - end of helix removed outlier: 4.542A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C 130 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 Processing helix chain 'C' and resid 158 through 161 No H-bonds generated for 'chain 'C' and resid 158 through 161' Processing helix chain 'C' and resid 178 through 205 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 217 through 240 Processing helix chain 'C' and resid 252 through 266 removed outlier: 5.377A pdb=" N GLY C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 291 Processing helix chain 'C' and resid 302 through 317 Processing helix chain 'C' and resid 319 through 322 No H-bonds generated for 'chain 'C' and resid 319 through 322' Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.945A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 375 removed outlier: 4.010A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 398 removed outlier: 3.540A pdb=" N PHE C 398 " --> pdb=" O PHE C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 415 Processing helix chain 'C' and resid 422 through 436 Processing helix chain 'C' and resid 440 through 442 No H-bonds generated for 'chain 'C' and resid 440 through 442' Processing helix chain 'C' and resid 447 through 462 removed outlier: 3.930A pdb=" N LEU C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N MET C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 474 Proline residue: C 469 - end of helix Processing helix chain 'C' and resid 476 through 490 Processing helix chain 'C' and resid 494 through 514 Processing helix chain 'C' and resid 533 through 536 No H-bonds generated for 'chain 'C' and resid 533 through 536' Processing helix chain 'C' and resid 556 through 570 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 670 through 685 Processing helix chain 'C' and resid 697 through 705 Processing helix chain 'C' and resid 724 through 730 Processing sheet with id= A, first strand: chain 'D' and resid 517 through 520 removed outlier: 4.399A pdb=" N SER D 517 " --> pdb=" O SER D 551 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER D 657 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LEU D 548 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL D 659 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE D 550 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP D 661 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N HIS D 689 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU D 660 " --> pdb=" O HIS D 689 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TYR D 691 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 521 through 523 Processing sheet with id= C, first strand: chain 'C' and resid 517 through 520 removed outlier: 4.399A pdb=" N SER C 517 " --> pdb=" O SER C 551 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER C 657 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LEU C 548 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 659 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE C 550 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ASP C 661 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N HIS C 689 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU C 660 " --> pdb=" O HIS C 689 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TYR C 691 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 521 through 523 514 hydrogen bonds defined for protein. 1518 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: 3.16 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1496 1.32 - 1.44: 2733 1.44 - 1.56: 6393 1.56 - 1.68: 12 1.68 - 1.81: 56 Bond restraints: 10690 Sorted by residual: bond pdb=" C10 LBN D 817 " pdb=" C7 LBN D 817 " ideal model delta sigma weight residual 1.523 1.455 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 LBN D 820 " pdb=" C7 LBN D 820 " ideal model delta sigma weight residual 1.523 1.455 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C10 LBN C 811 " pdb=" C7 LBN C 811 " ideal model delta sigma weight residual 1.523 1.456 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C36 LBN D 813 " pdb=" C37 LBN D 813 " ideal model delta sigma weight residual 1.524 1.462 0.062 2.00e-02 2.50e+03 9.62e+00 bond pdb=" O2 LBN D 813 " pdb=" P1 LBN D 813 " ideal model delta sigma weight residual 1.650 1.588 0.062 2.00e-02 2.50e+03 9.51e+00 ... (remaining 10685 not shown) Histogram of bond angle deviations from ideal: 94.94 - 102.75: 58 102.75 - 110.56: 3015 110.56 - 118.38: 5703 118.38 - 126.19: 5614 126.19 - 134.00: 112 Bond angle restraints: 14502 Sorted by residual: angle pdb=" O1 LBN C 816 " pdb=" P1 LBN C 816 " pdb=" O2 LBN C 816 " ideal model delta sigma weight residual 93.45 104.05 -10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1 LBN D 802 " pdb=" P1 LBN D 802 " pdb=" O2 LBN D 802 " ideal model delta sigma weight residual 93.45 104.04 -10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1 LBN D 812 " pdb=" P1 LBN D 812 " pdb=" O2 LBN D 812 " ideal model delta sigma weight residual 93.45 103.84 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" O1 LBN C 806 " pdb=" P1 LBN C 806 " pdb=" O2 LBN C 806 " ideal model delta sigma weight residual 93.45 103.80 -10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C ILE C 491 " pdb=" N LEU C 492 " pdb=" CA LEU C 492 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.35e+00 ... (remaining 14497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.83: 6808 33.83 - 67.66: 236 67.66 - 101.49: 58 101.49 - 135.32: 58 135.32 - 169.15: 6 Dihedral angle restraints: 7166 sinusoidal: 3616 harmonic: 3550 Sorted by residual: dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N HIS C 723 " pdb=" CA HIS C 723 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA VAL D 722 " pdb=" C VAL D 722 " pdb=" N HIS D 723 " pdb=" CA HIS D 723 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA THR C 404 " pdb=" C THR C 404 " pdb=" N THR C 405 " pdb=" CA THR C 405 " ideal model delta harmonic sigma weight residual -180.00 -153.99 -26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 7163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.972: 1756 0.972 - 1.944: 0 1.944 - 2.916: 0 2.916 - 3.888: 0 3.888 - 4.860: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" C2 LBN C 816 " pdb=" C1 LBN C 816 " pdb=" C3 LBN C 816 " pdb=" O7 LBN C 816 " both_signs ideal model delta sigma weight residual False -2.36 2.50 -4.86 2.00e-01 2.50e+01 5.91e+02 chirality pdb=" C2 LBN D 802 " pdb=" C1 LBN D 802 " pdb=" C3 LBN D 802 " pdb=" O7 LBN D 802 " both_signs ideal model delta sigma weight residual False -2.36 2.49 -4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C2 LBN D 813 " pdb=" C1 LBN D 813 " pdb=" C3 LBN D 813 " pdb=" O7 LBN D 813 " both_signs ideal model delta sigma weight residual False -2.36 -2.10 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1755 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 816 " -0.100 2.00e-02 2.50e+03 2.33e-01 5.43e+02 pdb=" C42 LBN C 816 " 0.314 2.00e-02 2.50e+03 pdb=" C5 LBN C 816 " -0.314 2.00e-02 2.50e+03 pdb=" C8 LBN C 816 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 802 " 0.101 2.00e-02 2.50e+03 2.33e-01 5.41e+02 pdb=" C42 LBN D 802 " -0.313 2.00e-02 2.50e+03 pdb=" C5 LBN D 802 " 0.313 2.00e-02 2.50e+03 pdb=" C8 LBN D 802 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 806 " 0.062 2.00e-02 2.50e+03 1.17e-01 1.38e+02 pdb=" C42 LBN C 806 " -0.154 2.00e-02 2.50e+03 pdb=" C5 LBN C 806 " 0.154 2.00e-02 2.50e+03 pdb=" C8 LBN C 806 " -0.062 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 636 2.74 - 3.28: 10442 3.28 - 3.82: 16263 3.82 - 4.36: 19831 4.36 - 4.90: 34119 Nonbonded interactions: 81291 Sorted by model distance: nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.197 2.520 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.197 2.520 nonbonded pdb=" NH1 ARG C 38 " pdb=" OE2 GLU C 701 " model vdw 2.257 2.520 nonbonded pdb=" OG1 THR C 132 " pdb=" OE1 GLU C 384 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR D 132 " pdb=" OE1 GLU D 384 " model vdw 2.274 2.440 ... (remaining 81286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 17 through 732 or resid 808 or (resid 813 and (name C25 or \ name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name C3 \ 2 or name C33)))) selection = (chain 'D' and (resid 17 through 732 or resid 808 or (resid 813 and (name C25 or \ name C26 or name C27 or name C28 or name C29 or name C30 or name C31 or name C3 \ 2 or name C33)))) } 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: 0.010 Normalize map: mean=0, sd=1: 0.440 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: 2.300 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 32.740 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.005 0.068 10690 Z= 0.283 Angle : 0.698 10.599 14502 Z= 0.329 Chirality : 0.170 4.860 1758 Planarity : 0.010 0.233 1650 Dihedral : 21.902 169.148 4878 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.19 % Allowed : 0.29 % Favored : 99.52 % 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: 1.04 (0.25), residues: 1210 helix: 1.80 (0.19), residues: 796 sheet: 1.68 (0.79), residues: 54 loop : -2.16 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 482 HIS 0.003 0.001 HIS D 698 PHE 0.026 0.001 PHE C 385 TYR 0.013 0.001 TYR C 323 ARG 0.002 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.151 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 1.0428 time to fit residues: 181.1059 Evaluate side-chains 106 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 266 ASN D 289 ASN C 35 GLN C 266 ASN C 289 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10690 Z= 0.150 Angle : 0.630 11.109 14502 Z= 0.293 Chirality : 0.044 0.242 1758 Planarity : 0.004 0.060 1650 Dihedral : 19.166 162.033 2730 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.82 % Allowed : 9.27 % Favored : 88.91 % 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: 1.26 (0.25), residues: 1210 helix: 1.97 (0.19), residues: 798 sheet: 1.73 (0.79), residues: 54 loop : -2.08 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 482 HIS 0.003 0.001 HIS C 698 PHE 0.022 0.001 PHE D 385 TYR 0.011 0.001 TYR C 371 ARG 0.001 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.098 Fit side-chains REVERT: D 463 MET cc_start: 0.7687 (mmm) cc_final: 0.7424 (mmm) REVERT: C 463 MET cc_start: 0.7689 (mmm) cc_final: 0.7433 (mmm) outliers start: 19 outliers final: 8 residues processed: 123 average time/residue: 0.9595 time to fit residues: 132.0345 Evaluate side-chains 113 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN C 35 GLN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10690 Z= 0.244 Angle : 0.647 11.230 14502 Z= 0.323 Chirality : 0.047 0.274 1758 Planarity : 0.005 0.067 1650 Dihedral : 17.923 157.486 2730 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.54 % Favored : 94.30 % Rotamer: Outliers : 2.87 % Allowed : 10.42 % Favored : 86.71 % 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: 0.87 (0.25), residues: 1210 helix: 1.57 (0.18), residues: 812 sheet: 2.26 (0.79), residues: 50 loop : -2.19 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 482 HIS 0.005 0.001 HIS C 698 PHE 0.027 0.002 PHE D 385 TYR 0.019 0.002 TYR D 315 ARG 0.003 0.000 ARG C 549 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 1.147 Fit side-chains REVERT: D 684 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: C 503 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6213 (mmt) REVERT: C 684 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7405 (tt0) outliers start: 30 outliers final: 15 residues processed: 138 average time/residue: 0.9953 time to fit residues: 151.1293 Evaluate side-chains 137 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 266 ASN D 289 ASN D 723 HIS C 35 GLN C 266 ASN C 289 ASN C 723 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10690 Z= 0.270 Angle : 0.664 10.667 14502 Z= 0.334 Chirality : 0.048 0.338 1758 Planarity : 0.005 0.073 1650 Dihedral : 17.146 154.391 2730 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.45 % Favored : 94.38 % Rotamer: Outliers : 3.44 % Allowed : 11.66 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.65 (0.24), residues: 1210 helix: 1.45 (0.18), residues: 808 sheet: 2.09 (0.76), residues: 50 loop : -2.34 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 74 HIS 0.004 0.001 HIS D 698 PHE 0.018 0.002 PHE D 385 TYR 0.016 0.002 TYR C 371 ARG 0.003 0.000 ARG C 549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.185 Fit side-chains REVERT: D 385 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: D 464 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8414 (mm110) REVERT: D 684 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: C 385 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: C 464 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8405 (mm110) REVERT: C 503 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6136 (mmt) REVERT: C 684 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7344 (tt0) outliers start: 36 outliers final: 18 residues processed: 138 average time/residue: 0.9569 time to fit residues: 145.3174 Evaluate side-chains 138 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 464 GLN Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN D 705 GLN C 35 GLN C 289 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10690 Z= 0.238 Angle : 0.634 9.368 14502 Z= 0.320 Chirality : 0.046 0.282 1758 Planarity : 0.005 0.074 1650 Dihedral : 16.709 154.687 2730 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 3.63 % Allowed : 13.29 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.75 (0.25), residues: 1210 helix: 1.55 (0.18), residues: 808 sheet: 1.94 (0.75), residues: 50 loop : -2.33 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.017 0.002 PHE D 385 TYR 0.019 0.002 TYR D 315 ARG 0.006 0.001 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.182 Fit side-chains REVERT: D 684 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: C 503 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6220 (mmt) REVERT: C 684 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7399 (tt0) outliers start: 38 outliers final: 24 residues processed: 136 average time/residue: 0.9610 time to fit residues: 143.9634 Evaluate side-chains 140 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 overall best weight: 1.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN C 35 GLN C 289 ASN C 383 GLN C 705 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10690 Z= 0.240 Angle : 0.644 11.349 14502 Z= 0.324 Chirality : 0.046 0.255 1758 Planarity : 0.005 0.073 1650 Dihedral : 16.355 154.272 2730 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 4.02 % Allowed : 13.19 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.78 (0.25), residues: 1210 helix: 1.64 (0.19), residues: 796 sheet: 1.86 (0.75), residues: 50 loop : -2.35 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 482 HIS 0.003 0.001 HIS D 698 PHE 0.016 0.002 PHE D 401 TYR 0.014 0.002 TYR C 371 ARG 0.005 0.000 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 1.165 Fit side-chains REVERT: D 385 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: D 684 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: C 155 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7633 (ttm) REVERT: C 385 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8406 (m-80) REVERT: C 503 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6221 (mmt) REVERT: C 684 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: C 701 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6869 (mt-10) outliers start: 42 outliers final: 23 residues processed: 139 average time/residue: 1.0276 time to fit residues: 157.0502 Evaluate side-chains 141 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 0.0570 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN D 464 GLN C 35 GLN C 289 ASN C 464 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10690 Z= 0.261 Angle : 0.662 11.704 14502 Z= 0.333 Chirality : 0.047 0.256 1758 Planarity : 0.005 0.073 1650 Dihedral : 16.168 156.304 2730 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 3.63 % Allowed : 13.67 % Favored : 82.70 % 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: 0.71 (0.25), residues: 1210 helix: 1.58 (0.19), residues: 796 sheet: 1.90 (0.75), residues: 50 loop : -2.36 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.018 0.002 PHE D 385 TYR 0.018 0.002 TYR C 315 ARG 0.006 0.001 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 109 time to evaluate : 1.117 Fit side-chains REVERT: D 473 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.7089 (mtp-110) REVERT: D 684 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: C 473 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7093 (mtp-110) REVERT: C 503 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6094 (mmp) REVERT: C 684 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: C 701 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6913 (mt-10) outliers start: 38 outliers final: 26 residues processed: 130 average time/residue: 1.0998 time to fit residues: 156.4406 Evaluate side-chains 141 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 432 MET Chi-restraints excluded: chain D residue 473 ARG Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 721 THR Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN D 464 GLN C 35 GLN C 289 ASN C 464 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10690 Z= 0.181 Angle : 0.587 9.074 14502 Z= 0.297 Chirality : 0.044 0.295 1758 Planarity : 0.005 0.070 1650 Dihedral : 15.356 156.260 2730 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.54 % Allowed : 13.86 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.04 (0.25), residues: 1210 helix: 1.81 (0.19), residues: 798 sheet: 1.43 (0.76), residues: 54 loop : -2.16 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 482 HIS 0.003 0.001 HIS C 656 PHE 0.015 0.001 PHE D 385 TYR 0.012 0.001 TYR C 371 ARG 0.006 0.000 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 110 time to evaluate : 1.195 Fit side-chains REVERT: D 155 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7515 (ttm) REVERT: D 684 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: C 503 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6161 (mmp) REVERT: C 684 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: C 701 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6825 (mt-10) outliers start: 37 outliers final: 16 residues processed: 132 average time/residue: 1.0369 time to fit residues: 150.0697 Evaluate side-chains 128 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 248 ASN Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN C 35 GLN C 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10690 Z= 0.164 Angle : 0.583 8.810 14502 Z= 0.295 Chirality : 0.044 0.342 1758 Planarity : 0.005 0.064 1650 Dihedral : 14.435 151.314 2730 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.58 % Allowed : 14.72 % Favored : 82.70 % 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: 1.19 (0.25), residues: 1210 helix: 1.93 (0.19), residues: 798 sheet: 1.43 (0.75), residues: 54 loop : -2.08 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.020 0.001 PHE C 385 TYR 0.022 0.001 TYR C 315 ARG 0.008 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.142 Fit side-chains REVERT: D 155 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7497 (ttm) REVERT: D 684 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.7022 (tt0) REVERT: C 442 LEU cc_start: 0.8523 (mm) cc_final: 0.8292 (mt) REVERT: C 684 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7019 (tt0) outliers start: 27 outliers final: 13 residues processed: 131 average time/residue: 0.9538 time to fit residues: 138.1801 Evaluate side-chains 125 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 0.0770 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10690 Z= 0.152 Angle : 0.558 8.611 14502 Z= 0.286 Chirality : 0.043 0.345 1758 Planarity : 0.005 0.063 1650 Dihedral : 13.545 142.245 2730 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.10 % Allowed : 15.30 % Favored : 82.60 % 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: 1.33 (0.26), residues: 1210 helix: 2.06 (0.19), residues: 796 sheet: 1.49 (0.77), residues: 54 loop : -2.07 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 482 HIS 0.002 0.001 HIS D 698 PHE 0.017 0.001 PHE D 141 TYR 0.011 0.001 TYR C 371 ARG 0.008 0.000 ARG D 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.177 Fit side-chains REVERT: D 155 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7475 (ttm) REVERT: D 442 LEU cc_start: 0.8537 (mm) cc_final: 0.8292 (mt) REVERT: D 684 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.7054 (tt0) REVERT: C 442 LEU cc_start: 0.8470 (mm) cc_final: 0.8231 (mt) REVERT: C 684 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.7057 (tt0) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 0.9712 time to fit residues: 136.9279 Evaluate side-chains 120 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 684 GLN Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 684 GLN Chi-restraints excluded: chain C residue 724 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.0670 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.0570 chunk 5 optimal weight: 10.0000 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN D 289 ASN C 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.180126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143654 restraints weight = 10607.733| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.46 r_work: 0.3417 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 10690 Z= 0.149 Angle : 0.549 8.601 14502 Z= 0.282 Chirality : 0.042 0.250 1758 Planarity : 0.005 0.062 1650 Dihedral : 12.999 133.902 2730 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.29 % Allowed : 15.20 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1210 helix: 2.05 (0.19), residues: 800 sheet: 1.54 (0.77), residues: 54 loop : -1.92 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 482 HIS 0.002 0.001 HIS C 656 PHE 0.018 0.001 PHE C 385 TYR 0.022 0.001 TYR D 315 ARG 0.008 0.000 ARG C 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3216.30 seconds wall clock time: 58 minutes 44.83 seconds (3524.83 seconds total)