Starting phenix.real_space_refine on Sun Apr 7 11:36:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/04_2024/8sh3_40479_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/04_2024/8sh3_40479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/04_2024/8sh3_40479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/04_2024/8sh3_40479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/04_2024/8sh3_40479_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh3_40479/04_2024/8sh3_40479_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.100 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: 6 Type Number sf(0) Gaussians I 4 10.91 5 P 6 5.49 5 S 36 5.16 5 C 7004 2.51 5 N 1542 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 10386 Number of models: 1 Model: "" Number of chains: 4 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: 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: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 438 Unusual residues: {'AV0': 2, 'CLR': 6, 'IOD': 2, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} 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: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 438 Unusual residues: {'AV0': 2, 'CLR': 6, 'IOD': 2, 'LBN': 9} Classifications: {'undetermined': 19} Link IDs: {None: 18} 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: 5.98, per 1000 atoms: 0.58 Number of scatterers: 10386 At special positions: 0 Unit cell: (85.078, 121.422, 105.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) I 4 52.95 S 36 16.00 P 6 15.00 O 1794 8.00 N 1542 7.00 C 7004 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: 4.01 Conformation dependent library (CDL) restraints added in 1.8 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: 53 helices and 2 sheets defined 63.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... 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 83 through 108 removed outlier: 3.738A pdb=" N LEU C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 107 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 3.877A 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: 4.188A pdb=" N ILE C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 4.238A 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 209 through 214 removed outlier: 4.084A pdb=" N VAL C 212 " --> pdb=" O GLY C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 240 Processing helix chain 'C' and resid 252 through 266 removed outlier: 5.301A pdb=" N GLY C 265 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 5.871A 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: 4.053A pdb=" N SER C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 375 removed outlier: 3.593A 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 447 through 474 removed outlier: 4.124A pdb=" N LYS C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N MET C 461 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL C 465 " --> pdb=" O MET C 461 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N CYS C 466 " --> pdb=" O PHE C 462 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) 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 686 removed outlier: 3.868A pdb=" N ILE C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 706 Processing helix chain 'C' and resid 724 through 730 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 83 through 108 removed outlier: 3.730A pdb=" N LEU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU D 107 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 3.839A 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: 4.227A pdb=" N ILE D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 4.261A 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 209 through 214 removed outlier: 4.076A pdb=" N VAL D 212 " --> pdb=" O GLY D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 240 Processing helix chain 'D' and resid 252 through 266 removed outlier: 5.263A pdb=" N GLY D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 5.857A 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 343 through 348 removed outlier: 4.067A pdb=" N SER D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 375 removed outlier: 3.652A pdb=" N SER D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.587A 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 447 through 474 removed outlier: 4.068A pdb=" N LYS D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLY D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N MET D 461 " --> pdb=" O ASN D 457 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL D 465 " --> pdb=" O MET D 461 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N CYS D 466 " --> pdb=" O PHE D 462 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL D 468 " --> pdb=" O GLN D 464 " (cutoff:3.500A) 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 686 removed outlier: 3.876A pdb=" N ILE D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 706 Processing helix chain 'D' and resid 724 through 730 Processing sheet with id= A, first strand: chain 'C' and resid 530 through 532 removed outlier: 4.273A pdb=" N ILE C 547 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N SER C 523 " --> pdb=" O VAL C 545 " (cutoff:3.500A) removed outlier: 12.667A pdb=" N VAL C 545 " --> pdb=" O SER C 523 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER C 657 " --> pdb=" O LYS C 546 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU C 548 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL C 659 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 7.586A 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: 6.253A pdb=" N HIS C 689 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU C 660 " --> pdb=" O HIS C 689 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR C 691 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.269A pdb=" N ILE D 547 " --> pdb=" O LEU D 521 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N SER D 523 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 12.668A pdb=" N VAL D 545 " --> pdb=" O SER D 523 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER D 657 " --> pdb=" O LYS D 546 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N LEU D 548 " --> pdb=" O SER D 657 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL D 659 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE D 550 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASP D 661 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N HIS D 689 " --> pdb=" O LEU D 658 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU D 660 " --> pdb=" O HIS D 689 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR D 691 " --> pdb=" O LEU D 660 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1557 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: 3.45 Time building geometry restraints manager: 4.36 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: 1531 1.32 - 1.44: 2634 1.44 - 1.57: 6373 1.57 - 1.69: 12 1.69 - 1.81: 56 Bond restraints: 10606 Sorted by residual: bond pdb=" O2 LBN C 813 " pdb=" P1 LBN C 813 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" O2 LBN D 813 " pdb=" P1 LBN D 813 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" O2 LBN C 811 " pdb=" P1 LBN C 811 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" O2 LBN C 810 " pdb=" P1 LBN C 810 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" O2 LBN D 810 " pdb=" P1 LBN D 810 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.25e+00 ... (remaining 10601 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.32: 290 106.32 - 113.23: 6114 113.23 - 120.15: 3712 120.15 - 127.06: 4189 127.06 - 133.98: 77 Bond angle restraints: 14382 Sorted by residual: angle pdb=" O1 LBN D 813 " pdb=" P1 LBN D 813 " pdb=" O2 LBN D 813 " ideal model delta sigma weight residual 93.45 104.45 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O1 LBN D 810 " pdb=" P1 LBN D 810 " pdb=" O2 LBN D 810 " ideal model delta sigma weight residual 93.45 104.17 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1 LBN C 810 " pdb=" P1 LBN C 810 " pdb=" O2 LBN C 810 " ideal model delta sigma weight residual 93.45 104.14 -10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" O1 LBN C 813 " pdb=" P1 LBN C 813 " pdb=" O2 LBN C 813 " 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 811 " pdb=" P1 LBN D 811 " pdb=" O2 LBN D 811 " ideal model delta sigma weight residual 93.45 103.76 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 14377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.53: 6833 34.53 - 69.07: 207 69.07 - 103.60: 45 103.60 - 138.14: 56 138.14 - 172.67: 9 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 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+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 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" C1 LBN D 810 " pdb=" O1 LBN D 810 " pdb=" P1 LBN D 810 " pdb=" O3 LBN D 810 " ideal model delta sinusoidal sigma weight residual 275.40 102.73 172.67 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 - 4.856: 2 Chirality restraints: 1758 Sorted by residual: chirality pdb=" C2 LBN C 813 " pdb=" C1 LBN C 813 " pdb=" C3 LBN C 813 " pdb=" O7 LBN C 813 " 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 2.46 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C2 LBN D 811 " pdb=" C1 LBN D 811 " pdb=" C3 LBN D 811 " pdb=" O7 LBN D 811 " both_signs ideal model delta sigma weight residual False -2.36 -2.60 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1755 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 813 " -0.100 2.00e-02 2.50e+03 2.28e-01 5.20e+02 pdb=" C42 LBN C 813 " 0.307 2.00e-02 2.50e+03 pdb=" C5 LBN C 813 " -0.307 2.00e-02 2.50e+03 pdb=" C8 LBN C 813 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN D 813 " 0.217 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" C42 LBN D 813 " -0.215 2.00e-02 2.50e+03 pdb=" C5 LBN D 813 " -0.219 2.00e-02 2.50e+03 pdb=" C8 LBN D 813 " 0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN C 810 " 0.095 2.00e-02 2.50e+03 2.09e-01 4.35e+02 pdb=" C42 LBN C 810 " -0.279 2.00e-02 2.50e+03 pdb=" C5 LBN C 810 " 0.279 2.00e-02 2.50e+03 pdb=" C8 LBN C 810 " -0.095 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 840 2.74 - 3.30: 11094 3.30 - 3.85: 18731 3.85 - 4.41: 23532 4.41 - 4.96: 38845 Nonbonded interactions: 93042 Sorted by model distance: nonbonded pdb=" OH TYR D 78 " pdb=" OD2 ASP D 87 " model vdw 2.186 2.440 nonbonded pdb=" O PRO C 553 " pdb=" ND2 ASN C 558 " model vdw 2.196 2.520 nonbonded pdb=" O PRO D 553 " pdb=" ND2 ASN D 558 " model vdw 2.196 2.520 nonbonded pdb=" OH TYR C 78 " pdb=" OD2 ASP C 87 " model vdw 2.204 2.440 nonbonded pdb=" O PHE C 555 " pdb=" N VAL C 559 " model vdw 2.253 2.520 ... (remaining 93037 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' selection = chain 'D' } 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: 1.550 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: 6.270 Check model and map are aligned: 0.150 Set scattering table: 0.140 Process input model: 31.700 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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: 52.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.004 0.054 10606 Z= 0.253 Angle : 0.651 11.001 14382 Z= 0.310 Chirality : 0.169 4.856 1758 Planarity : 0.011 0.228 1638 Dihedral : 21.604 172.671 4862 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % 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: 1.02 (0.25), residues: 1210 helix: 1.74 (0.19), residues: 802 sheet: 1.57 (0.77), residues: 36 loop : -1.88 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.017 0.001 PHE D 141 TYR 0.012 0.001 TYR C 371 ARG 0.002 0.000 ARG D 185 *********************** 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 132 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.045 Fit side-chains REVERT: C 79 ARG cc_start: 0.6657 (mmm-85) cc_final: 0.6188 (mtp180) REVERT: C 440 LYS cc_start: 0.7426 (ttmm) cc_final: 0.6726 (mptt) REVERT: D 35 GLN cc_start: 0.7316 (tt0) cc_final: 0.7094 (tm-30) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.9996 time to fit residues: 145.1327 Evaluate side-chains 106 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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: 0.7980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN D 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10606 Z= 0.296 Angle : 0.704 10.451 14382 Z= 0.334 Chirality : 0.047 0.205 1758 Planarity : 0.005 0.082 1638 Dihedral : 19.049 177.126 2714 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 1.82 % Allowed : 7.46 % 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: 0.77 (0.24), residues: 1210 helix: 1.40 (0.18), residues: 814 sheet: 1.83 (0.70), residues: 34 loop : -1.71 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 74 HIS 0.003 0.001 HIS D 698 PHE 0.022 0.002 PHE C 141 TYR 0.019 0.002 TYR C 556 ARG 0.003 0.000 ARG C 581 *********************** 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 134 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.096 Fit side-chains REVERT: C 35 GLN cc_start: 0.7373 (tt0) cc_final: 0.7077 (tm-30) REVERT: C 79 ARG cc_start: 0.6713 (mmm-85) cc_final: 0.6245 (mtp180) REVERT: C 307 THR cc_start: 0.8052 (m) cc_final: 0.7844 (p) REVERT: C 440 LYS cc_start: 0.7411 (ttmm) cc_final: 0.6750 (mptt) REVERT: D 35 GLN cc_start: 0.7330 (tt0) cc_final: 0.7038 (tm-30) REVERT: D 307 THR cc_start: 0.8039 (m) cc_final: 0.7831 (p) REVERT: D 322 ASN cc_start: 0.7703 (m110) cc_final: 0.7465 (m110) REVERT: D 440 LYS cc_start: 0.7359 (ttmm) cc_final: 0.6693 (mptt) outliers start: 19 outliers final: 9 residues processed: 127 average time/residue: 1.0836 time to fit residues: 151.2982 Evaluate side-chains 116 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 0.0000 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 ASN D 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10606 Z= 0.209 Angle : 0.604 9.939 14382 Z= 0.293 Chirality : 0.045 0.294 1758 Planarity : 0.005 0.082 1638 Dihedral : 17.398 172.806 2714 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.72 % Allowed : 9.18 % Favored : 89.10 % 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: 0.88 (0.24), residues: 1210 helix: 1.56 (0.18), residues: 812 sheet: 1.77 (0.68), residues: 34 loop : -1.85 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.018 0.001 PHE D 141 TYR 0.013 0.001 TYR D 371 ARG 0.002 0.000 ARG C 185 *********************** 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 126 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.085 Fit side-chains REVERT: C 35 GLN cc_start: 0.7356 (tt0) cc_final: 0.7094 (tm-30) REVERT: C 307 THR cc_start: 0.8035 (m) cc_final: 0.7825 (p) REVERT: C 440 LYS cc_start: 0.7426 (ttmm) cc_final: 0.6791 (mptt) REVERT: C 655 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6890 (mp) REVERT: D 35 GLN cc_start: 0.7327 (tt0) cc_final: 0.7062 (tm-30) REVERT: D 385 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: D 440 LYS cc_start: 0.7329 (ttmm) cc_final: 0.6683 (mptt) outliers start: 18 outliers final: 9 residues processed: 123 average time/residue: 0.9789 time to fit residues: 132.6313 Evaluate side-chains 113 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 545 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 689 HIS D 322 ASN D 689 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10606 Z= 0.311 Angle : 0.676 8.877 14382 Z= 0.330 Chirality : 0.049 0.358 1758 Planarity : 0.005 0.081 1638 Dihedral : 16.609 179.163 2714 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.71 % Rotamer: Outliers : 2.77 % Allowed : 10.33 % Favored : 86.90 % 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: 0.68 (0.24), residues: 1210 helix: 1.35 (0.18), residues: 812 sheet: 1.65 (0.69), residues: 34 loop : -1.77 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 74 HIS 0.003 0.001 HIS C 656 PHE 0.021 0.002 PHE C 141 TYR 0.018 0.002 TYR D 371 ARG 0.004 0.000 ARG C 581 *********************** 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 144 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.055 Fit side-chains REVERT: C 35 GLN cc_start: 0.7378 (tt0) cc_final: 0.7030 (tm-30) REVERT: C 79 ARG cc_start: 0.6962 (mmm160) cc_final: 0.6283 (mtp180) REVERT: C 307 THR cc_start: 0.8092 (m) cc_final: 0.7776 (p) REVERT: C 321 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7563 (ptmt) REVERT: C 385 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: C 440 LYS cc_start: 0.7461 (ttmm) cc_final: 0.6828 (mptt) REVERT: C 655 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6953 (mp) REVERT: D 35 GLN cc_start: 0.7253 (tt0) cc_final: 0.6950 (tm-30) REVERT: D 38 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6751 (ttt180) REVERT: D 385 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: D 440 LYS cc_start: 0.7366 (ttmm) cc_final: 0.6722 (mptt) outliers start: 29 outliers final: 14 residues processed: 133 average time/residue: 0.9435 time to fit residues: 138.6048 Evaluate side-chains 130 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10606 Z= 0.193 Angle : 0.602 8.177 14382 Z= 0.293 Chirality : 0.046 0.348 1758 Planarity : 0.005 0.084 1638 Dihedral : 15.672 175.836 2714 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.20 % Allowed : 12.33 % Favored : 85.47 % 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 (0.24), residues: 1210 helix: 1.56 (0.19), residues: 812 sheet: 1.64 (0.67), residues: 34 loop : -1.86 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.019 0.001 PHE D 141 TYR 0.014 0.002 TYR C 323 ARG 0.003 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 130 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.062 Fit side-chains REVERT: C 35 GLN cc_start: 0.7358 (tt0) cc_final: 0.7095 (tm-30) REVERT: C 385 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: C 440 LYS cc_start: 0.7435 (ttmm) cc_final: 0.6806 (mptt) REVERT: C 655 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6937 (mp) REVERT: D 35 GLN cc_start: 0.7340 (tt0) cc_final: 0.7107 (tm-30) REVERT: D 38 ARG cc_start: 0.7077 (ttp80) cc_final: 0.6777 (ttt180) REVERT: D 385 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: D 440 LYS cc_start: 0.7404 (ttmm) cc_final: 0.6770 (mptt) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 0.9881 time to fit residues: 135.0500 Evaluate side-chains 120 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10606 Z= 0.225 Angle : 0.610 8.480 14382 Z= 0.299 Chirality : 0.046 0.357 1758 Planarity : 0.005 0.084 1638 Dihedral : 14.727 168.677 2714 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 2.20 % Allowed : 12.81 % Favored : 84.99 % 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 (0.24), residues: 1210 helix: 1.49 (0.18), residues: 814 sheet: 1.74 (0.69), residues: 34 loop : -1.70 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 74 HIS 0.002 0.001 HIS D 656 PHE 0.022 0.001 PHE C 141 TYR 0.015 0.002 TYR C 371 ARG 0.002 0.000 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 133 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.183 Fit side-chains REVERT: C 35 GLN cc_start: 0.7390 (tt0) cc_final: 0.7120 (tm-30) REVERT: C 79 ARG cc_start: 0.7027 (mmm160) cc_final: 0.6278 (mtp180) REVERT: C 385 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: C 440 LYS cc_start: 0.7431 (ttmm) cc_final: 0.6816 (mptt) REVERT: C 655 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6927 (mp) REVERT: D 35 GLN cc_start: 0.7317 (tt0) cc_final: 0.7078 (tm-30) REVERT: D 385 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: D 440 LYS cc_start: 0.7416 (ttmm) cc_final: 0.6786 (mptt) outliers start: 23 outliers final: 16 residues processed: 128 average time/residue: 0.9879 time to fit residues: 139.7141 Evaluate side-chains 123 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10606 Z= 0.211 Angle : 0.595 8.722 14382 Z= 0.294 Chirality : 0.045 0.307 1758 Planarity : 0.005 0.083 1638 Dihedral : 14.194 165.739 2714 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.49 % Allowed : 12.91 % Favored : 84.61 % 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: 0.82 (0.24), residues: 1210 helix: 1.50 (0.18), residues: 812 sheet: 1.84 (0.67), residues: 34 loop : -1.83 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.020 0.001 PHE D 141 TYR 0.013 0.002 TYR C 371 ARG 0.003 0.000 ARG D 185 *********************** 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 132 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.972 Fit side-chains REVERT: C 79 ARG cc_start: 0.6999 (mmm160) cc_final: 0.6260 (mtp180) REVERT: C 385 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: C 440 LYS cc_start: 0.7428 (ttmm) cc_final: 0.6812 (mptt) REVERT: C 655 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.6940 (mp) REVERT: D 35 GLN cc_start: 0.7391 (tt0) cc_final: 0.7185 (tm-30) REVERT: D 38 ARG cc_start: 0.7101 (tpp80) cc_final: 0.6769 (ttt180) REVERT: D 385 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: D 440 LYS cc_start: 0.7413 (ttmm) cc_final: 0.6786 (mptt) outliers start: 26 outliers final: 15 residues processed: 127 average time/residue: 0.9563 time to fit residues: 134.0575 Evaluate side-chains 121 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10606 Z= 0.201 Angle : 0.592 10.137 14382 Z= 0.294 Chirality : 0.044 0.251 1758 Planarity : 0.005 0.083 1638 Dihedral : 13.702 161.243 2714 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.10 % Allowed : 13.48 % Favored : 84.42 % 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: 0.86 (0.24), residues: 1210 helix: 1.52 (0.18), residues: 812 sheet: 1.93 (0.67), residues: 34 loop : -1.79 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.020 0.001 PHE D 141 TYR 0.013 0.001 TYR C 371 ARG 0.003 0.000 ARG C 185 *********************** 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 126 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.095 Fit side-chains REVERT: C 79 ARG cc_start: 0.7041 (mmm160) cc_final: 0.6307 (mtp180) REVERT: C 385 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: C 440 LYS cc_start: 0.7419 (ttmm) cc_final: 0.6805 (mptt) REVERT: C 655 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6925 (mp) REVERT: D 385 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: D 440 LYS cc_start: 0.7417 (ttmm) cc_final: 0.6784 (mptt) outliers start: 22 outliers final: 17 residues processed: 121 average time/residue: 1.0140 time to fit residues: 134.7773 Evaluate side-chains 120 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 115 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 GLN D 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10606 Z= 0.180 Angle : 0.571 9.200 14382 Z= 0.286 Chirality : 0.043 0.204 1758 Planarity : 0.005 0.082 1638 Dihedral : 13.118 156.511 2714 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.39 % Allowed : 13.48 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1210 helix: 1.56 (0.18), residues: 812 sheet: 2.00 (0.67), residues: 34 loop : -1.76 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.020 0.001 PHE D 141 TYR 0.014 0.001 TYR D 105 ARG 0.002 0.000 ARG D 185 *********************** 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 134 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.987 Fit side-chains REVERT: C 79 ARG cc_start: 0.7036 (mmm160) cc_final: 0.6301 (mtp180) REVERT: C 385 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: C 440 LYS cc_start: 0.7420 (ttmm) cc_final: 0.6796 (mptt) REVERT: C 655 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6897 (mp) REVERT: D 38 ARG cc_start: 0.7132 (tpp80) cc_final: 0.6815 (ttt180) REVERT: D 385 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7044 (m-80) REVERT: D 440 LYS cc_start: 0.7406 (ttmm) cc_final: 0.6780 (mptt) REVERT: D 463 MET cc_start: 0.8309 (mmt) cc_final: 0.8044 (tpt) outliers start: 25 outliers final: 17 residues processed: 125 average time/residue: 0.9949 time to fit residues: 136.7901 Evaluate side-chains 125 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 80 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.003 0.057 10606 Z= 0.180 Angle : 0.584 10.868 14382 Z= 0.290 Chirality : 0.043 0.203 1758 Planarity : 0.004 0.079 1638 Dihedral : 12.803 151.813 2714 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.39 % Allowed : 14.34 % Favored : 83.27 % 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: 0.96 (0.24), residues: 1210 helix: 1.58 (0.18), residues: 812 sheet: 2.10 (0.68), residues: 34 loop : -1.75 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.019 0.001 PHE D 141 TYR 0.015 0.001 TYR D 105 ARG 0.002 0.000 ARG C 185 ********************** 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 132 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 1.182 Fit side-chains REVERT: C 385 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: C 440 LYS cc_start: 0.7419 (ttmm) cc_final: 0.6797 (mptt) REVERT: C 655 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6898 (mp) REVERT: D 38 ARG cc_start: 0.7120 (tpp80) cc_final: 0.6820 (ttt180) REVERT: D 385 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: D 440 LYS cc_start: 0.7409 (ttmm) cc_final: 0.6780 (mptt) REVERT: D 463 MET cc_start: 0.8283 (mmt) cc_final: 0.8058 (tpt) outliers start: 25 outliers final: 16 residues processed: 122 average time/residue: 1.0725 time to fit residues: 144.3810 Evaluate side-chains 122 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 137 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 556 TYR Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 0.0000 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.174235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140697 restraints weight = 7732.834| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.46 r_work: 0.3567 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10606 Z= 0.177 Angle : 0.587 12.950 14382 Z= 0.292 Chirality : 0.043 0.203 1758 Planarity : 0.004 0.079 1638 Dihedral : 12.606 148.158 2714 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.91 % Allowed : 14.91 % Favored : 83.17 % 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: 0.99 (0.25), residues: 1210 helix: 1.60 (0.18), residues: 812 sheet: 2.16 (0.69), residues: 34 loop : -1.72 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 482 HIS 0.002 0.001 HIS D 656 PHE 0.019 0.001 PHE D 141 TYR 0.015 0.001 TYR C 105 ARG 0.002 0.000 ARG D 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3247.17 seconds wall clock time: 59 minutes 30.12 seconds (3570.12 seconds total)