Starting phenix.real_space_refine on Sun Apr 7 11:48:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sie_40507/04_2024/8sie_40507_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sie_40507/04_2024/8sie_40507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sie_40507/04_2024/8sie_40507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sie_40507/04_2024/8sie_40507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sie_40507/04_2024/8sie_40507_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sie_40507/04_2024/8sie_40507_updated.pdb" } resolution = 2.7 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= 0.007 sd= 0.148 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 C 7008 2.51 5 N 1542 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 217": "OD1" <-> "OD2" Residue "D TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "C TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 704": "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: 10398 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: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 444 Unusual residues: {'AV0': 1, 'BCT': 2, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 7 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: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 444 Unusual residues: {'AV0': 1, 'BCT': 2, 'CLR': 6, 'DMU': 1, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 7 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: 6.15, per 1000 atoms: 0.59 Number of scatterers: 10398 At special positions: 0 Unit cell: (90.688, 122.304, 107.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 6 15.00 O 1806 8.00 N 1542 7.00 C 7008 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 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! Possible link ignored !!! !!! HETATM10300 C18 DMU C 818 45.138 61.404 32.360 1.00 58.03 C !!! !!! HETATM 9856 C18 DMU D 818 44.791 59.955 32.316 1.00 58.05 C !!! !!! N-linked glycan : False !!! !!! O-linked glycan : False !!! !!! Glycan-glycan : True !!! !!! No oxygen atom found !!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.23 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 2 sheets defined 63.7% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 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 108 removed outlier: 3.892A pdb=" N LEU D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 130 Proline residue: D 123 - end of helix removed outlier: 4.288A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.229A 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 206 Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 217 through 239 Processing helix chain 'D' and resid 252 through 266 removed outlier: 5.473A pdb=" N GLY D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 6.227A 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: 4.192A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 375 removed outlier: 3.933A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 398 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: 4.426A pdb=" N LYS D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.992A 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 491 removed outlier: 3.680A pdb=" N ILE D 490 " --> pdb=" O CYS D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 514 removed outlier: 3.653A pdb=" N LEU D 499 " --> pdb=" O ASP D 495 " (cutoff:3.500A) 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 731 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 108 removed outlier: 3.896A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 130 Proline residue: C 123 - end of helix removed outlier: 4.271A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.239A 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 206 Processing helix chain 'C' and resid 210 through 213 Processing helix chain 'C' and resid 217 through 239 Processing helix chain 'C' and resid 252 through 266 removed outlier: 5.464A pdb=" N GLY C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 6.195A 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: 4.188A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 375 removed outlier: 3.944A pdb=" N SER C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 398 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: 4.436A pdb=" N LYS C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 5.001A 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 491 Processing helix chain 'C' and resid 494 through 514 removed outlier: 3.523A pdb=" N LEU C 499 " --> pdb=" O ASP C 495 " (cutoff:3.500A) 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 731 Processing sheet with id= A, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.305A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.844A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER D 657 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU D 548 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL D 659 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N PHE D 550 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP D 661 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS D 689 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU D 660 " --> pdb=" O HIS D 689 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR D 691 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.300A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.844A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER C 657 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N LEU C 548 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 659 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE C 550 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP C 661 " --> pdb=" O PHE C 550 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS C 689 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU C 660 " --> pdb=" O HIS C 689 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR C 691 " --> pdb=" O LEU C 660 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1539 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: 2.86 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1550 1.32 - 1.44: 2631 1.44 - 1.57: 6369 1.57 - 1.69: 12 1.69 - 1.81: 56 Bond restraints: 10618 Sorted by residual: bond pdb=" C BCT D 816 " pdb=" O3 BCT D 816 " ideal model delta sigma weight residual 1.389 1.263 0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C BCT C 816 " pdb=" O3 BCT C 816 " ideal model delta sigma weight residual 1.389 1.264 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C BCT C 816 " pdb=" O1 BCT C 816 " ideal model delta sigma weight residual 1.236 1.332 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C BCT D 816 " pdb=" O1 BCT D 816 " ideal model delta sigma weight residual 1.236 1.332 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C BCT D 817 " pdb=" O3 BCT D 817 " ideal model delta sigma weight residual 1.389 1.333 0.056 2.00e-02 2.50e+03 7.87e+00 ... (remaining 10613 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.30: 284 106.30 - 113.24: 6122 113.24 - 120.18: 3753 120.18 - 127.11: 4153 127.11 - 134.05: 82 Bond angle restraints: 14394 Sorted by residual: angle pdb=" N ILE D 490 " pdb=" CA ILE D 490 " pdb=" C ILE D 490 " ideal model delta sigma weight residual 111.81 108.09 3.72 8.60e-01 1.35e+00 1.87e+01 angle pdb=" O1 BCT C 816 " pdb=" C BCT C 816 " pdb=" O2 BCT C 816 " ideal model delta sigma weight residual 129.92 117.87 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O1 BCT D 816 " pdb=" C BCT D 816 " pdb=" O2 BCT D 816 " ideal model delta sigma weight residual 129.92 117.90 12.02 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O1 LBN D 806 " pdb=" P1 LBN D 806 " pdb=" O2 LBN D 806 " ideal model delta sigma weight residual 93.45 104.03 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O1 LBN C 807 " pdb=" P1 LBN C 807 " pdb=" O2 LBN C 807 " ideal model delta sigma weight residual 93.45 104.03 -10.58 3.00e+00 1.11e-01 1.24e+01 ... (remaining 14389 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 6800 34.22 - 68.45: 248 68.45 - 102.67: 35 102.67 - 136.89: 57 136.89 - 171.12: 10 Dihedral angle restraints: 7150 sinusoidal: 3600 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 180.00 151.31 28.69 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 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CBS AV0 D 819 " pdb=" C1 AV0 D 819 " pdb=" O1 AV0 D 819 " pdb=" O5 AV0 D 819 " ideal model delta sinusoidal sigma weight residual 85.89 -85.23 171.12 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 7147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.971: 1756 0.971 - 1.943: 0 1.943 - 2.914: 0 2.914 - 3.885: 0 3.885 - 4.857: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" C2 LBN D 815 " pdb=" C1 LBN D 815 " pdb=" C3 LBN D 815 " pdb=" O7 LBN D 815 " 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 C 801 " pdb=" C1 LBN C 801 " pdb=" C3 LBN C 801 " pdb=" O7 LBN C 801 " both_signs ideal model delta sigma weight residual False -2.36 2.49 -4.85 2.00e-01 2.50e+01 5.89e+02 chirality pdb=" C2 LBN D 807 " pdb=" C1 LBN D 807 " pdb=" C3 LBN D 807 " pdb=" O7 LBN D 807 " both_signs ideal model delta sigma weight residual False -2.36 -2.59 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1755 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 801 " -0.101 2.00e-02 2.50e+03 2.46e-01 6.03e+02 pdb=" C42 LBN C 801 " 0.331 2.00e-02 2.50e+03 pdb=" C5 LBN C 801 " -0.333 2.00e-02 2.50e+03 pdb=" C8 LBN C 801 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 815 " -0.242 2.00e-02 2.50e+03 2.40e-01 5.75e+02 pdb=" C42 LBN D 815 " 0.247 2.00e-02 2.50e+03 pdb=" C5 LBN D 815 " 0.232 2.00e-02 2.50e+03 pdb=" C8 LBN D 815 " -0.238 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 806 " -0.049 2.00e-02 2.50e+03 9.20e-02 8.46e+01 pdb=" C42 LBN D 806 " 0.120 2.00e-02 2.50e+03 pdb=" C5 LBN D 806 " -0.120 2.00e-02 2.50e+03 pdb=" C8 LBN D 806 " 0.049 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 3 2.17 - 2.85: 3384 2.85 - 3.54: 14627 3.54 - 4.22: 23265 4.22 - 4.90: 42300 Nonbonded interactions: 83579 Sorted by model distance: nonbonded pdb=" C18 DMU D 818 " pdb=" C18 DMU C 818 " model vdw 1.491 3.840 nonbonded pdb=" O16 DMU D 818 " pdb=" C18 DMU C 818 " model vdw 2.131 3.440 nonbonded pdb=" OG SER C 90 " pdb=" O GLN C 413 " model vdw 2.171 2.440 nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.175 2.520 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.176 2.520 ... (remaining 83574 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 802 through 805 or (resid 807 and \ (name C1 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40 or name O1 or name O2 or name O3 or name O4 or name O7 or name O8 o \ r name P1 )) or (resid 810 through 811 and (name C10 or name C31 or name C32 or \ name C33 or name C4 or name C7 )) or (resid 812 through 813 and (name C10 or nam \ e C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 )) o \ r resid 814 through 819)) selection = (chain 'D' and (resid 17 through 732 or resid 802 through 805 or (resid 807 and \ (name C1 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C40 or name O1 or name O2 or name O3 or name O4 or name O7 or name O8 o \ r name P1 )) or (resid 810 through 811 and (name C10 or name C31 or name C32 or \ name C33 or name C4 or name C7 )) or (resid 812 through 813 and (name C10 or nam \ e C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 )) o \ r (resid 814 through 815 and (name C10 or name C25 or name C26 or name C27 or na \ me C28 or name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or \ name C7 )) or resid 816 through 819)) } 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: 0.610 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: 3.870 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.290 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 0.126 10618 Z= 0.297 Angle : 0.672 12.052 14394 Z= 0.322 Chirality : 0.170 4.857 1758 Planarity : 0.010 0.246 1642 Dihedral : 21.892 171.116 4862 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.19 % Allowed : 0.10 % Favored : 99.71 % 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: 1.29 (0.25), residues: 1210 helix: 2.02 (0.19), residues: 802 sheet: 1.16 (0.61), residues: 54 loop : -2.08 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.002 0.001 HIS C 728 PHE 0.029 0.001 PHE D 385 TYR 0.012 0.001 TYR D 323 ARG 0.005 0.000 ARG C 730 *********************** 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 130 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 1.149 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 1.3049 time to fit residues: 179.4095 Evaluate side-chains 103 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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: 0.6980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 49 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10618 Z= 0.165 Angle : 0.591 11.266 14394 Z= 0.271 Chirality : 0.043 0.212 1758 Planarity : 0.003 0.030 1642 Dihedral : 18.296 156.302 2714 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.53 % Allowed : 6.02 % Favored : 92.45 % 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: 1.39 (0.25), residues: 1210 helix: 2.10 (0.19), residues: 804 sheet: 1.58 (0.61), residues: 50 loop : -2.10 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.003 0.001 HIS D 728 PHE 0.015 0.001 PHE C 555 TYR 0.017 0.001 TYR D 556 ARG 0.005 0.000 ARG C 730 *********************** 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 123 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.046 Fit side-chains REVERT: D 315 TYR cc_start: 0.7097 (t80) cc_final: 0.6836 (t80) REVERT: D 576 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.5640 (mpt90) REVERT: C 315 TYR cc_start: 0.7092 (t80) cc_final: 0.6835 (t80) REVERT: C 576 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.5645 (mpt90) outliers start: 16 outliers final: 6 residues processed: 112 average time/residue: 1.3192 time to fit residues: 159.2354 Evaluate side-chains 101 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10618 Z= 0.216 Angle : 0.540 8.483 14394 Z= 0.267 Chirality : 0.044 0.318 1758 Planarity : 0.003 0.030 1642 Dihedral : 16.961 160.355 2714 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.39 % Allowed : 6.88 % Favored : 90.73 % 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: 1.37 (0.25), residues: 1210 helix: 2.10 (0.19), residues: 800 sheet: 1.50 (0.59), residues: 50 loop : -2.07 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.003 0.001 HIS C 698 PHE 0.016 0.002 PHE D 401 TYR 0.011 0.001 TYR C 556 ARG 0.002 0.000 ARG D 38 *********************** 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 118 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 1.004 Fit side-chains REVERT: D 576 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.5466 (mpt90) REVERT: C 461 MET cc_start: 0.8194 (mtm) cc_final: 0.7960 (mtm) REVERT: C 503 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6293 (mmt) REVERT: C 576 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.5472 (mpt90) outliers start: 25 outliers final: 13 residues processed: 104 average time/residue: 1.1692 time to fit residues: 131.9250 Evaluate side-chains 101 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 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 246 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10618 Z= 0.233 Angle : 0.558 8.202 14394 Z= 0.278 Chirality : 0.044 0.275 1758 Planarity : 0.004 0.034 1642 Dihedral : 15.645 147.900 2714 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.73 % Allowed : 6.41 % Favored : 89.87 % 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: 1.30 (0.25), residues: 1210 helix: 2.03 (0.19), residues: 800 sheet: 1.34 (0.59), residues: 50 loop : -2.05 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.017 0.002 PHE C 401 TYR 0.013 0.002 TYR D 323 ARG 0.003 0.000 ARG C 185 *********************** 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 124 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 1.063 Fit side-chains REVERT: D 576 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.5385 (mpt90) REVERT: C 320 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6896 (tt0) REVERT: C 576 ARG cc_start: 0.6742 (OUTLIER) cc_final: 0.5378 (mpt90) outliers start: 39 outliers final: 23 residues processed: 113 average time/residue: 1.1361 time to fit residues: 139.5824 Evaluate side-chains 105 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 79 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 560 ASP Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 87 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10618 Z= 0.185 Angle : 0.514 8.572 14394 Z= 0.256 Chirality : 0.043 0.257 1758 Planarity : 0.003 0.029 1642 Dihedral : 14.716 149.539 2714 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.73 % Allowed : 8.70 % Favored : 87.57 % 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: 1.45 (0.25), residues: 1210 helix: 2.12 (0.19), residues: 802 sheet: 1.33 (0.59), residues: 50 loop : -1.93 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 PHE 0.015 0.001 PHE C 401 TYR 0.014 0.001 TYR D 323 ARG 0.002 0.000 ARG C 185 *********************** 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 124 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 1.116 Fit side-chains REVERT: D 576 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5394 (mpt90) REVERT: C 576 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.5388 (mpt90) outliers start: 39 outliers final: 20 residues processed: 112 average time/residue: 1.0628 time to fit residues: 130.2596 Evaluate side-chains 104 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10618 Z= 0.337 Angle : 0.624 10.396 14394 Z= 0.311 Chirality : 0.047 0.269 1758 Planarity : 0.004 0.040 1642 Dihedral : 14.947 143.308 2714 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.11 % Allowed : 8.89 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.24), residues: 1210 helix: 1.81 (0.19), residues: 800 sheet: 1.10 (0.59), residues: 50 loop : -1.99 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.004 0.001 HIS D 698 PHE 0.019 0.002 PHE C 401 TYR 0.015 0.002 TYR C 323 ARG 0.005 0.001 ARG C 581 *********************** 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 131 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 88 time to evaluate : 1.036 Fit side-chains REVERT: D 576 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.5383 (mpt90) REVERT: C 320 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: C 576 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.5380 (mpt90) outliers start: 43 outliers final: 24 residues processed: 118 average time/residue: 1.1814 time to fit residues: 151.2912 Evaluate side-chains 108 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 81 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 117 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 248 ASN D 464 GLN D 684 GLN C 246 ASN C 464 GLN C 684 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10618 Z= 0.199 Angle : 0.534 8.463 14394 Z= 0.267 Chirality : 0.044 0.317 1758 Planarity : 0.003 0.035 1642 Dihedral : 14.202 144.741 2714 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.54 % Allowed : 10.80 % Favored : 85.66 % 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: 1.31 (0.25), residues: 1210 helix: 2.00 (0.19), residues: 802 sheet: 1.16 (0.59), residues: 50 loop : -1.93 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 482 HIS 0.002 0.001 HIS C 698 PHE 0.015 0.001 PHE C 401 TYR 0.015 0.001 TYR C 323 ARG 0.004 0.000 ARG D 581 *********************** 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 115 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 78 time to evaluate : 1.134 Fit side-chains REVERT: D 320 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6867 (tt0) REVERT: D 576 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5381 (mpt90) REVERT: C 320 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: C 576 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5379 (mpt90) outliers start: 37 outliers final: 23 residues processed: 105 average time/residue: 1.2244 time to fit residues: 139.7505 Evaluate side-chains 103 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 464 GLN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10618 Z= 0.279 Angle : 0.584 10.040 14394 Z= 0.292 Chirality : 0.046 0.356 1758 Planarity : 0.004 0.044 1642 Dihedral : 14.040 141.052 2714 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.35 % Allowed : 11.38 % Favored : 85.28 % 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: 1.18 (0.24), residues: 1210 helix: 1.87 (0.19), residues: 802 sheet: 1.13 (0.59), residues: 50 loop : -1.91 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.017 0.002 PHE D 401 TYR 0.016 0.002 TYR D 323 ARG 0.004 0.001 ARG D 581 *********************** 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 114 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 79 time to evaluate : 1.089 Fit side-chains REVERT: D 320 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: D 576 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5381 (mpt90) REVERT: C 320 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: C 503 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6392 (mmt) REVERT: C 576 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5382 (mpt90) outliers start: 35 outliers final: 23 residues processed: 106 average time/residue: 1.1517 time to fit residues: 133.5450 Evaluate side-chains 107 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 576 ARG 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: 0.0870 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 0.0570 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 248 ASN D 464 GLN D 684 GLN C 246 ASN C 248 ASN C 684 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10618 Z= 0.144 Angle : 0.481 6.841 14394 Z= 0.243 Chirality : 0.042 0.300 1758 Planarity : 0.003 0.044 1642 Dihedral : 13.165 143.875 2714 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.58 % Allowed : 12.33 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1210 helix: 2.16 (0.19), residues: 804 sheet: 1.35 (0.62), residues: 50 loop : -1.81 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 482 HIS 0.002 0.001 HIS D 656 PHE 0.014 0.001 PHE D 385 TYR 0.015 0.001 TYR D 323 ARG 0.003 0.000 ARG D 730 *********************** 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 109 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 1.139 Fit side-chains REVERT: D 320 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6798 (tt0) REVERT: D 564 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7506 (tmmt) REVERT: D 576 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.5360 (mpt90) REVERT: C 320 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6778 (tt0) REVERT: C 503 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6285 (mmt) REVERT: C 564 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7504 (tmmt) REVERT: C 576 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.5352 (mpt90) outliers start: 27 outliers final: 13 residues processed: 101 average time/residue: 1.3451 time to fit residues: 147.4449 Evaluate side-chains 98 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 564 LYS Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 349 MET Chi-restraints excluded: chain C residue 385 PHE 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 559 VAL Chi-restraints excluded: chain C residue 564 LYS Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10618 Z= 0.254 Angle : 0.563 10.481 14394 Z= 0.283 Chirality : 0.044 0.307 1758 Planarity : 0.004 0.044 1642 Dihedral : 13.187 137.641 2714 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.68 % Allowed : 12.52 % Favored : 84.80 % 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: 1.36 (0.25), residues: 1210 helix: 2.04 (0.19), residues: 802 sheet: 1.20 (0.59), residues: 50 loop : -1.89 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 482 HIS 0.003 0.001 HIS C 698 PHE 0.018 0.002 PHE D 401 TYR 0.016 0.002 TYR D 323 ARG 0.003 0.001 ARG D 581 ********************** 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 106 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 1.058 Fit side-chains REVERT: D 320 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6843 (tt0) REVERT: D 576 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.5400 (mpt90) REVERT: C 320 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: C 503 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6394 (mmt) REVERT: C 576 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.5404 (mpt90) outliers start: 28 outliers final: 14 residues processed: 98 average time/residue: 1.3156 time to fit residues: 139.3991 Evaluate side-chains 94 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 320 GLU Chi-restraints excluded: chain D residue 349 MET Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 576 ARG Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 320 GLU Chi-restraints excluded: chain C residue 385 PHE 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 559 VAL Chi-restraints excluded: chain C residue 576 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.0570 chunk 89 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 ASN D 248 ASN D 684 GLN C 246 ASN C 684 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.160682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126274 restraints weight = 11910.827| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.70 r_work: 0.3271 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10618 Z= 0.155 Angle : 0.485 7.764 14394 Z= 0.246 Chirality : 0.041 0.232 1758 Planarity : 0.003 0.043 1642 Dihedral : 12.724 139.036 2714 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.91 % Allowed : 13.19 % Favored : 84.89 % 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 (0.25), residues: 1210 helix: 2.17 (0.19), residues: 802 sheet: 1.31 (0.61), residues: 50 loop : -1.85 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 482 HIS 0.002 0.001 HIS D 656 PHE 0.013 0.001 PHE D 385 TYR 0.014 0.001 TYR D 323 ARG 0.003 0.000 ARG D 730 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3252.81 seconds wall clock time: 59 minutes 36.77 seconds (3576.77 seconds total)