Starting phenix.real_space_refine on Fri Feb 14 15:49:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ayg_7020/02_2025/6ayg_7020.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ayg_7020/02_2025/6ayg_7020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ayg_7020/02_2025/6ayg_7020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ayg_7020/02_2025/6ayg_7020.map" model { file = "/net/cci-nas-00/data/ceres_data/6ayg_7020/02_2025/6ayg_7020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ayg_7020/02_2025/6ayg_7020.cif" } resolution = 4.65 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= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 6648 2.51 5 N 1896 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10456 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 2614 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PTRANS': 8, 'TRANS': 430} Chain breaks: 5 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1300 Unresolved non-hydrogen dihedrals: 808 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 12, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 462 Restraints were copied for chains: C, B, D Time building chain proxies: 5.02, per 1000 atoms: 0.48 Number of scatterers: 10456 At special positions: 0 Unit cell: (100.35, 100.35, 105.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1876 8.00 N 1896 7.00 C 6648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 66.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 60 through 103 removed outlier: 3.613A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 5.014A pdb=" N TYR A 137 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.508A pdb=" N VAL A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 302 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 352 through 366 Processing helix chain 'A' and resid 370 through 397 removed outlier: 3.905A pdb=" N SER A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 433 Proline residue: A 410 - end of helix removed outlier: 3.815A pdb=" N MET A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 removed outlier: 4.629A pdb=" N TYR A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.536A pdb=" N ALA A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.524A pdb=" N ILE A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 513 removed outlier: 3.577A pdb=" N PHE A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 60 through 103 removed outlier: 3.613A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 5.014A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.508A pdb=" N VAL B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 302 Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 341 through 352 Processing helix chain 'B' and resid 352 through 366 Processing helix chain 'B' and resid 370 through 397 removed outlier: 3.905A pdb=" N SER B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 433 Proline residue: B 410 - end of helix removed outlier: 3.814A pdb=" N MET B 421 " --> pdb=" O CYS B 417 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 439 removed outlier: 4.629A pdb=" N TYR B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 456 Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.537A pdb=" N ALA B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.524A pdb=" N ILE B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 removed outlier: 3.577A pdb=" N PHE B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 526 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 49 through 54 Processing helix chain 'C' and resid 60 through 103 removed outlier: 3.612A pdb=" N ALA C 64 " --> pdb=" O PRO C 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 5.014A pdb=" N TYR C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.508A pdb=" N VAL C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 Processing helix chain 'C' and resid 306 through 318 Processing helix chain 'C' and resid 341 through 352 Processing helix chain 'C' and resid 352 through 366 Processing helix chain 'C' and resid 370 through 397 removed outlier: 3.905A pdb=" N SER C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 433 Proline residue: C 410 - end of helix removed outlier: 3.815A pdb=" N MET C 421 " --> pdb=" O CYS C 417 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 439 removed outlier: 4.629A pdb=" N TYR C 437 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP C 439 " --> pdb=" O GLY C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 456 Processing helix chain 'C' and resid 459 through 466 removed outlier: 3.537A pdb=" N ALA C 465 " --> pdb=" O PHE C 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 491 removed outlier: 3.524A pdb=" N ILE C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 513 removed outlier: 3.578A pdb=" N PHE C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 526 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 49 through 54 Processing helix chain 'D' and resid 60 through 103 removed outlier: 3.612A pdb=" N ALA D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 140 removed outlier: 5.014A pdb=" N TYR D 137 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.508A pdb=" N VAL D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 302 Processing helix chain 'D' and resid 306 through 318 Processing helix chain 'D' and resid 341 through 352 Processing helix chain 'D' and resid 352 through 366 Processing helix chain 'D' and resid 370 through 397 removed outlier: 3.904A pdb=" N SER D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 433 Proline residue: D 410 - end of helix removed outlier: 3.815A pdb=" N MET D 421 " --> pdb=" O CYS D 417 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 439 removed outlier: 4.630A pdb=" N TYR D 437 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP D 439 " --> pdb=" O GLY D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 456 Processing helix chain 'D' and resid 459 through 466 removed outlier: 3.537A pdb=" N ALA D 465 " --> pdb=" O PHE D 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.524A pdb=" N ILE D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 513 removed outlier: 3.577A pdb=" N PHE D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 188 removed outlier: 4.244A pdb=" N THR A 215 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA3, first strand: chain 'B' and resid 181 through 188 removed outlier: 4.244A pdb=" N THR B 215 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AA5, first strand: chain 'C' and resid 181 through 188 removed outlier: 4.244A pdb=" N THR C 215 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AA7, first strand: chain 'D' and resid 181 through 188 removed outlier: 4.244A pdb=" N THR D 215 " --> pdb=" O HIS D 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 167 through 168 949 hydrogen bonds defined for protein. 2799 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: 3.61 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3636 1.36 - 1.49: 3104 1.49 - 1.63: 3888 1.63 - 1.76: 0 1.76 - 1.89: 48 Bond restraints: 10676 Sorted by residual: bond pdb=" CB PHE D 102 " pdb=" CG PHE D 102 " ideal model delta sigma weight residual 1.502 1.428 0.074 2.30e-02 1.89e+03 1.02e+01 bond pdb=" CB PHE B 102 " pdb=" CG PHE B 102 " ideal model delta sigma weight residual 1.502 1.429 0.073 2.30e-02 1.89e+03 1.02e+01 bond pdb=" CB PHE C 102 " pdb=" CG PHE C 102 " ideal model delta sigma weight residual 1.502 1.429 0.073 2.30e-02 1.89e+03 1.02e+01 bond pdb=" CB PHE A 102 " pdb=" CG PHE A 102 " ideal model delta sigma weight residual 1.502 1.429 0.073 2.30e-02 1.89e+03 1.01e+01 bond pdb=" CB PHE B 288 " pdb=" CG PHE B 288 " ideal model delta sigma weight residual 1.502 1.575 -0.073 2.30e-02 1.89e+03 1.01e+01 ... (remaining 10671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 14026 3.14 - 6.28: 595 6.28 - 9.41: 94 9.41 - 12.55: 29 12.55 - 15.69: 8 Bond angle restraints: 14752 Sorted by residual: angle pdb=" N ILE B 493 " pdb=" CA ILE B 493 " pdb=" C ILE B 493 " ideal model delta sigma weight residual 110.42 122.48 -12.06 9.60e-01 1.09e+00 1.58e+02 angle pdb=" N ILE A 493 " pdb=" CA ILE A 493 " pdb=" C ILE A 493 " ideal model delta sigma weight residual 110.42 122.47 -12.05 9.60e-01 1.09e+00 1.58e+02 angle pdb=" N ILE C 493 " pdb=" CA ILE C 493 " pdb=" C ILE C 493 " ideal model delta sigma weight residual 110.42 122.47 -12.05 9.60e-01 1.09e+00 1.58e+02 angle pdb=" N ILE D 493 " pdb=" CA ILE D 493 " pdb=" C ILE D 493 " ideal model delta sigma weight residual 110.42 122.44 -12.02 9.60e-01 1.09e+00 1.57e+02 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 111.07 121.28 -10.21 1.07e+00 8.73e-01 9.11e+01 ... (remaining 14747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.26: 5477 13.26 - 26.52: 364 26.52 - 39.78: 107 39.78 - 53.04: 16 53.04 - 66.30: 8 Dihedral angle restraints: 5972 sinusoidal: 804 harmonic: 5168 Sorted by residual: dihedral pdb=" CA LYS C 466 " pdb=" C LYS C 466 " pdb=" N MET C 467 " pdb=" CA MET C 467 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LYS A 466 " pdb=" C LYS A 466 " pdb=" N MET A 467 " pdb=" CA MET A 467 " ideal model delta harmonic sigma weight residual -180.00 -156.72 -23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LYS D 466 " pdb=" C LYS D 466 " pdb=" N MET D 467 " pdb=" CA MET D 467 " ideal model delta harmonic sigma weight residual -180.00 -156.72 -23.28 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 5969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1352 0.076 - 0.152: 318 0.152 - 0.228: 50 0.228 - 0.304: 8 0.304 - 0.380: 16 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CG LEU C 482 " pdb=" CB LEU C 482 " pdb=" CD1 LEU C 482 " pdb=" CD2 LEU C 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CG LEU B 482 " pdb=" CB LEU B 482 " pdb=" CD1 LEU B 482 " pdb=" CD2 LEU B 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CG LEU D 482 " pdb=" CB LEU D 482 " pdb=" CD1 LEU D 482 " pdb=" CD2 LEU D 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1741 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 48 " -0.104 5.00e-02 4.00e+02 1.73e-01 4.81e+01 pdb=" N PRO B 49 " 0.300 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.103 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 48 " 0.104 5.00e-02 4.00e+02 1.73e-01 4.80e+01 pdb=" N PRO A 49 " -0.300 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 48 " 0.104 5.00e-02 4.00e+02 1.73e-01 4.80e+01 pdb=" N PRO D 49 " -0.300 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.093 5.00e-02 4.00e+02 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 907 2.72 - 3.27: 11353 3.27 - 3.81: 15814 3.81 - 4.36: 18109 4.36 - 4.90: 28141 Nonbonded interactions: 74324 Sorted by model distance: nonbonded pdb=" O PHE D 489 " pdb=" N ILE D 493 " model vdw 2.180 3.120 nonbonded pdb=" O PHE C 489 " pdb=" N ILE C 493 " model vdw 2.204 3.120 nonbonded pdb=" O PHE B 489 " pdb=" N ILE B 493 " model vdw 2.204 3.120 nonbonded pdb=" O PHE A 489 " pdb=" N ILE A 493 " model vdw 2.205 3.120 nonbonded pdb=" O LEU A 488 " pdb=" CB MET A 492 " model vdw 2.252 3.440 ... (remaining 74319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.480 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.013 0.093 10676 Z= 0.887 Angle : 1.563 15.688 14752 Z= 1.006 Chirality : 0.073 0.380 1744 Planarity : 0.013 0.173 2004 Dihedral : 11.749 66.300 2596 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.67 % Favored : 91.86 % Rotamer: Outliers : 1.09 % Allowed : 15.22 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.16), residues: 1708 helix: -3.18 (0.12), residues: 996 sheet: -1.38 (0.27), residues: 264 loop : -2.32 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.006 TRP C 61 HIS 0.016 0.006 HIS C 252 PHE 0.045 0.005 PHE C 291 TYR 0.043 0.008 TYR D 481 ARG 0.016 0.004 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.1292 time to fit residues: 7.7453 Evaluate side-chains 39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0020 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 81 optimal weight: 30.0000 chunk 100 optimal weight: 0.0060 chunk 156 optimal weight: 6.9990 overall best weight: 0.7006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.057080 restraints weight = 19159.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.057927 restraints weight = 14688.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.058429 restraints weight = 12082.437| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10676 Z= 0.182 Angle : 0.586 6.548 14752 Z= 0.343 Chirality : 0.041 0.142 1744 Planarity : 0.005 0.053 2004 Dihedral : 5.555 20.032 1808 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: -1.94 (0.18), residues: 1708 helix: -0.98 (0.14), residues: 1052 sheet: -1.10 (0.27), residues: 264 loop : -1.67 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 475 HIS 0.006 0.001 HIS C 252 PHE 0.020 0.002 PHE B 489 TYR 0.019 0.003 TYR A 481 ARG 0.005 0.001 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9395 (tp-100) cc_final: 0.9090 (tp-100) REVERT: A 385 TRP cc_start: 0.9512 (m100) cc_final: 0.8947 (m-90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0892 time to fit residues: 5.5781 Evaluate side-chains 39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 152 optimal weight: 8.9990 chunk 17 optimal weight: 50.0000 chunk 106 optimal weight: 0.0980 chunk 127 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 142 optimal weight: 40.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.055255 restraints weight = 17604.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056147 restraints weight = 13094.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056914 restraints weight = 10566.106| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10676 Z= 0.150 Angle : 0.478 5.763 14752 Z= 0.275 Chirality : 0.039 0.117 1744 Planarity : 0.004 0.051 2004 Dihedral : 4.786 19.721 1808 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: 0.02 (0.19), residues: 1708 helix: 0.83 (0.15), residues: 1068 sheet: -0.55 (0.27), residues: 268 loop : -1.74 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 431 HIS 0.003 0.001 HIS C 252 PHE 0.027 0.002 PHE C 489 TYR 0.012 0.001 TYR B 123 ARG 0.002 0.001 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.388 Fit side-chains REVERT: A 76 GLN cc_start: 0.9251 (tp-100) cc_final: 0.9018 (tp-100) REVERT: A 255 ARG cc_start: 0.7987 (ptt180) cc_final: 0.7221 (tpp-160) REVERT: A 385 TRP cc_start: 0.9340 (m100) cc_final: 0.8770 (m-10) REVERT: A 431 TRP cc_start: 0.8788 (t-100) cc_final: 0.8579 (t60) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0986 time to fit residues: 5.8506 Evaluate side-chains 39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 121 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 134 optimal weight: 0.8980 overall best weight: 4.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.066971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.053761 restraints weight = 20185.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.054670 restraints weight = 15349.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055248 restraints weight = 12325.043| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10676 Z= 0.204 Angle : 0.514 6.703 14752 Z= 0.295 Chirality : 0.040 0.121 1744 Planarity : 0.004 0.047 2004 Dihedral : 4.561 18.816 1808 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: 0.61 (0.20), residues: 1708 helix: 1.41 (0.15), residues: 1080 sheet: -0.63 (0.27), residues: 272 loop : -1.76 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 385 HIS 0.003 0.001 HIS C 100 PHE 0.020 0.002 PHE A 489 TYR 0.010 0.001 TYR C 398 ARG 0.001 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9416 (ttm) cc_final: 0.9001 (ttm) REVERT: A 385 TRP cc_start: 0.9478 (m100) cc_final: 0.8901 (m-10) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0988 time to fit residues: 5.2554 Evaluate side-chains 36 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 113 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 17 optimal weight: 50.0000 chunk 93 optimal weight: 30.0000 chunk 16 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.0010 chunk 112 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055440 restraints weight = 19617.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056309 restraints weight = 14975.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.056931 restraints weight = 12257.582| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10676 Z= 0.139 Angle : 0.454 6.114 14752 Z= 0.254 Chirality : 0.039 0.115 1744 Planarity : 0.003 0.048 2004 Dihedral : 4.213 17.771 1808 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: 1.38 (0.20), residues: 1708 helix: 2.05 (0.16), residues: 1076 sheet: -0.32 (0.28), residues: 272 loop : -1.58 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 431 HIS 0.002 0.001 HIS C 252 PHE 0.017 0.001 PHE A 489 TYR 0.008 0.001 TYR B 123 ARG 0.002 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.328 Fit side-chains REVERT: A 72 MET cc_start: 0.9431 (ttm) cc_final: 0.8954 (ttp) REVERT: A 385 TRP cc_start: 0.9428 (m100) cc_final: 0.8923 (m-10) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0898 time to fit residues: 5.4097 Evaluate side-chains 37 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 84 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 31 optimal weight: 0.0970 chunk 106 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 40.0000 chunk 43 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 overall best weight: 3.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.065616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051758 restraints weight = 18675.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.052648 restraints weight = 13618.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.053399 restraints weight = 10861.358| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10676 Z= 0.192 Angle : 0.507 6.333 14752 Z= 0.286 Chirality : 0.041 0.199 1744 Planarity : 0.003 0.045 2004 Dihedral : 4.215 17.037 1808 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 1.48 (0.21), residues: 1708 helix: 2.17 (0.16), residues: 1076 sheet: -0.40 (0.29), residues: 272 loop : -1.59 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 385 HIS 0.002 0.001 HIS C 100 PHE 0.016 0.002 PHE D 485 TYR 0.009 0.001 TYR B 511 ARG 0.001 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.309 Fit side-chains REVERT: A 72 MET cc_start: 0.9473 (ttm) cc_final: 0.8960 (ttp) REVERT: A 385 TRP cc_start: 0.9472 (m100) cc_final: 0.8904 (m-10) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0749 time to fit residues: 4.1903 Evaluate side-chains 34 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 114 optimal weight: 0.0870 chunk 46 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 167 optimal weight: 30.0000 chunk 150 optimal weight: 50.0000 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 162 optimal weight: 0.0030 overall best weight: 4.0174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.065169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051519 restraints weight = 19242.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.052458 restraints weight = 14238.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053117 restraints weight = 11330.004| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10676 Z= 0.179 Angle : 0.476 5.997 14752 Z= 0.274 Chirality : 0.040 0.155 1744 Planarity : 0.003 0.044 2004 Dihedral : 4.132 17.123 1808 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 1.70 (0.21), residues: 1708 helix: 2.43 (0.16), residues: 1072 sheet: -0.41 (0.29), residues: 272 loop : -1.71 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 385 HIS 0.002 0.001 HIS A 100 PHE 0.026 0.002 PHE A 452 TYR 0.014 0.001 TYR B 106 ARG 0.001 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.286 Fit side-chains REVERT: A 72 MET cc_start: 0.9474 (ttm) cc_final: 0.8954 (ttp) REVERT: A 385 TRP cc_start: 0.9507 (m100) cc_final: 0.8915 (m-10) REVERT: A 405 LEU cc_start: 0.8942 (mm) cc_final: 0.8700 (mm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0723 time to fit residues: 4.1327 Evaluate side-chains 34 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 17 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 40.0000 chunk 160 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.065981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.052129 restraints weight = 18621.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.053093 restraints weight = 13652.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053780 restraints weight = 10830.793| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10676 Z= 0.137 Angle : 0.452 5.940 14752 Z= 0.253 Chirality : 0.039 0.117 1744 Planarity : 0.003 0.044 2004 Dihedral : 3.988 16.986 1808 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.21), residues: 1708 helix: 2.52 (0.16), residues: 1088 sheet: -0.29 (0.30), residues: 272 loop : -1.70 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 385 HIS 0.002 0.001 HIS C 252 PHE 0.019 0.001 PHE D 485 TYR 0.009 0.001 TYR D 106 ARG 0.001 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.282 Fit side-chains REVERT: A 72 MET cc_start: 0.9353 (ttm) cc_final: 0.8912 (ttp) REVERT: A 385 TRP cc_start: 0.9266 (m100) cc_final: 0.8767 (m-10) REVERT: A 405 LEU cc_start: 0.9047 (mm) cc_final: 0.8774 (mm) REVERT: A 431 TRP cc_start: 0.9314 (t60) cc_final: 0.8704 (t60) REVERT: A 452 PHE cc_start: 0.9351 (t80) cc_final: 0.9145 (t80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0707 time to fit residues: 4.0511 Evaluate side-chains 35 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 171 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 157 optimal weight: 0.0040 chunk 113 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 overall best weight: 3.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.065363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.051513 restraints weight = 18735.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.052405 restraints weight = 13647.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.053123 restraints weight = 10880.896| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10676 Z= 0.179 Angle : 0.472 5.818 14752 Z= 0.271 Chirality : 0.040 0.162 1744 Planarity : 0.003 0.043 2004 Dihedral : 4.027 16.915 1808 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: 1.91 (0.21), residues: 1708 helix: 2.59 (0.16), residues: 1084 sheet: -0.26 (0.31), residues: 272 loop : -1.85 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 385 HIS 0.002 0.001 HIS C 100 PHE 0.015 0.002 PHE D 489 TYR 0.013 0.001 TYR D 106 ARG 0.001 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.282 Fit side-chains REVERT: C 72 MET cc_start: 0.9480 (ttm) cc_final: 0.9053 (ttp) REVERT: C 405 LEU cc_start: 0.8983 (mm) cc_final: 0.8751 (mm) REVERT: C 431 TRP cc_start: 0.9414 (t60) cc_final: 0.8778 (t60) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0716 time to fit residues: 3.9461 Evaluate side-chains 33 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 20.0000 chunk 71 optimal weight: 0.0010 chunk 113 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.0030 chunk 95 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.066124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.052151 restraints weight = 18264.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.053108 restraints weight = 13472.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053772 restraints weight = 10740.291| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10676 Z= 0.136 Angle : 0.446 5.365 14752 Z= 0.247 Chirality : 0.039 0.119 1744 Planarity : 0.003 0.043 2004 Dihedral : 3.850 16.524 1808 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.95 (0.21), residues: 1708 helix: 2.56 (0.16), residues: 1092 sheet: -0.21 (0.32), residues: 272 loop : -1.72 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 385 HIS 0.002 0.001 HIS D 252 PHE 0.022 0.001 PHE D 452 TYR 0.009 0.001 TYR D 106 ARG 0.001 0.000 ARG C 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.291 Fit side-chains REVERT: D 72 MET cc_start: 0.9439 (ttm) cc_final: 0.9053 (ttp) REVERT: D 405 LEU cc_start: 0.8944 (mm) cc_final: 0.8697 (mm) REVERT: D 431 TRP cc_start: 0.9410 (t60) cc_final: 0.8802 (t60) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0789 time to fit residues: 4.3664 Evaluate side-chains 34 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 81 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.064176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.050771 restraints weight = 18565.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051706 restraints weight = 13222.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.052400 restraints weight = 10390.210| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10676 Z= 0.208 Angle : 0.475 5.131 14752 Z= 0.275 Chirality : 0.039 0.122 1744 Planarity : 0.003 0.042 2004 Dihedral : 3.987 16.370 1808 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.21), residues: 1708 helix: 2.03 (0.16), residues: 1076 sheet: -0.50 (0.32), residues: 272 loop : -2.01 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 385 HIS 0.003 0.001 HIS C 100 PHE 0.017 0.002 PHE B 489 TYR 0.013 0.001 TYR A 106 ARG 0.001 0.000 ARG D 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1615.34 seconds wall clock time: 29 minutes 49.29 seconds (1789.29 seconds total)