Starting phenix.real_space_refine on Tue Nov 18 02:49:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ayg_7020/11_2025/6ayg_7020.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ayg_7020/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ayg_7020/11_2025/6ayg_7020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ayg_7020/11_2025/6ayg_7020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ayg_7020/11_2025/6ayg_7020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ayg_7020/11_2025/6ayg_7020.map" } resolution = 4.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'ARG:plan': 12, 'ASN:plan1': 16, 'GLU:plan': 15, 'PHE:plan': 12, 'ASP:plan': 22, 'TYR:plan': 9, 'GLN:plan1': 16, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 462 Restraints were copied for chains: B, C, D Time building chain proxies: 2.04, per 1000 atoms: 0.20 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: 1.00 Conformation dependent library (CDL) restraints added in 528.0 milliseconds 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: 0.38 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: 1.69 Time building geometry restraints manager: 1.30 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 0.260 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- 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= 0.695 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.016 0.004 ARG D 56 TYR 0.043 0.008 TYR D 481 PHE 0.045 0.005 PHE C 291 TRP 0.039 0.006 TRP C 61 HIS 0.016 0.006 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.01288 (10676) covalent geometry : angle 1.56337 (14752) hydrogen bonds : bond 0.14207 ( 949) hydrogen bonds : angle 11.91395 ( 2799) *********************** 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 : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.0545 time to fit residues: 3.3019 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 : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 0.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 50.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.0670 overall best weight: 1.0128 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.070861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.057256 restraints weight = 19393.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058109 restraints weight = 14813.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058660 restraints weight = 12136.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.059134 restraints weight = 10584.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059313 restraints weight = 9509.990| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3451 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= 0.149 Angle : 0.578 6.452 14752 Z= 0.336 Chirality : 0.041 0.151 1744 Planarity : 0.005 0.058 2004 Dihedral : 5.402 19.549 1808 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 1708 helix: -0.81 (0.14), residues: 1056 sheet: -1.17 (0.27), residues: 276 loop : -1.58 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 56 TYR 0.024 0.002 TYR C 239 PHE 0.027 0.002 PHE B 489 TRP 0.024 0.002 TRP C 475 HIS 0.006 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00251 (10676) covalent geometry : angle 0.57770 (14752) hydrogen bonds : bond 0.04691 ( 949) hydrogen bonds : angle 6.08704 ( 2799) *********************** 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 : 0.099 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9044 (tp-100) REVERT: A 385 TRP cc_start: 0.9492 (m100) cc_final: 0.8915 (m-90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0412 time to fit residues: 2.5607 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 48 optimal weight: 7.9990 chunk 138 optimal weight: 20.0000 chunk 15 optimal weight: 0.0270 chunk 86 optimal weight: 30.0000 chunk 131 optimal weight: 0.0770 chunk 141 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.070836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.057350 restraints weight = 19794.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.058204 restraints weight = 15333.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.058755 restraints weight = 12525.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059237 restraints weight = 10907.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.059555 restraints weight = 9773.748| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10676 Z= 0.116 Angle : 0.477 5.784 14752 Z= 0.271 Chirality : 0.039 0.118 1744 Planarity : 0.004 0.050 2004 Dihedral : 4.701 19.684 1808 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 1708 helix: 1.04 (0.15), residues: 1064 sheet: -0.61 (0.27), residues: 268 loop : -1.67 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 56 TYR 0.011 0.001 TYR B 123 PHE 0.012 0.001 PHE B 497 TRP 0.020 0.002 TRP B 431 HIS 0.003 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00198 (10676) covalent geometry : angle 0.47740 (14752) hydrogen bonds : bond 0.03609 ( 949) hydrogen bonds : angle 4.95103 ( 2799) *********************** 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 47 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.112 Fit side-chains REVERT: A 72 MET cc_start: 0.9154 (mmm) cc_final: 0.8868 (ttm) REVERT: A 76 GLN cc_start: 0.9375 (tp-100) cc_final: 0.9078 (tp-100) REVERT: A 255 ARG cc_start: 0.7910 (ptt180) cc_final: 0.6984 (tpp-160) REVERT: A 385 TRP cc_start: 0.9455 (m100) cc_final: 0.8657 (m-10) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0440 time to fit residues: 2.7193 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 : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 124 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 146 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 28 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 7 optimal weight: 30.0000 chunk 81 optimal weight: 30.0000 overall best weight: 8.6390 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.062806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049430 restraints weight = 19430.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.050331 restraints weight = 14162.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.050970 restraints weight = 11218.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.051448 restraints weight = 9485.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051791 restraints weight = 8348.970| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10676 Z= 0.319 Angle : 0.637 9.693 14752 Z= 0.381 Chirality : 0.042 0.145 1744 Planarity : 0.005 0.049 2004 Dihedral : 5.074 19.141 1808 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.19), residues: 1708 helix: 0.58 (0.15), residues: 1080 sheet: -1.09 (0.28), residues: 276 loop : -1.78 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 414 TYR 0.014 0.002 TYR C 398 PHE 0.030 0.003 PHE A 485 TRP 0.017 0.003 TRP B 385 HIS 0.006 0.002 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00543 (10676) covalent geometry : angle 0.63721 (14752) hydrogen bonds : bond 0.04882 ( 949) hydrogen bonds : angle 5.52303 ( 2799) *********************** 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 37 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.105 Fit side-chains REVERT: A 72 MET cc_start: 0.9264 (mmm) cc_final: 0.9004 (tpp) REVERT: A 76 GLN cc_start: 0.9416 (tp-100) cc_final: 0.9171 (tp-100) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0294 time to fit residues: 1.6057 Evaluate side-chains 31 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 158 optimal weight: 20.0000 chunk 129 optimal weight: 30.0000 chunk 63 optimal weight: 0.7980 chunk 56 optimal weight: 30.0000 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 127 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.067249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054117 restraints weight = 19926.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.054907 restraints weight = 15139.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055517 restraints weight = 12402.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055707 restraints weight = 10713.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056125 restraints weight = 9945.868| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10676 Z= 0.123 Angle : 0.464 5.825 14752 Z= 0.264 Chirality : 0.040 0.119 1744 Planarity : 0.003 0.046 2004 Dihedral : 4.447 16.811 1808 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1708 helix: 1.78 (0.16), residues: 1076 sheet: -0.72 (0.29), residues: 268 loop : -1.69 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 56 TYR 0.008 0.001 TYR C 481 PHE 0.018 0.001 PHE D 485 TRP 0.018 0.002 TRP C 385 HIS 0.002 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00209 (10676) covalent geometry : angle 0.46363 (14752) hydrogen bonds : bond 0.03409 ( 949) hydrogen bonds : angle 4.74727 ( 2799) *********************** 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 39 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.118 Fit side-chains REVERT: A 76 GLN cc_start: 0.9259 (tp-100) cc_final: 0.9046 (tp-100) REVERT: A 385 TRP cc_start: 0.9498 (m100) cc_final: 0.8790 (m-10) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0297 time to fit residues: 1.7136 Evaluate side-chains 32 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 44 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 50 optimal weight: 30.0000 chunk 18 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3205 r_free = 0.3205 target = 0.063835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.050640 restraints weight = 19267.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051563 restraints weight = 13874.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.052234 restraints weight = 10966.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052605 restraints weight = 9210.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052605 restraints weight = 8244.389| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10676 Z= 0.211 Angle : 0.525 6.191 14752 Z= 0.305 Chirality : 0.041 0.124 1744 Planarity : 0.004 0.045 2004 Dihedral : 4.473 17.370 1808 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1708 helix: 1.60 (0.15), residues: 1080 sheet: -0.84 (0.29), residues: 268 loop : -1.61 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 479 TYR 0.009 0.001 TYR C 398 PHE 0.038 0.002 PHE C 291 TRP 0.021 0.002 TRP C 431 HIS 0.003 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00366 (10676) covalent geometry : angle 0.52531 (14752) hydrogen bonds : bond 0.04031 ( 949) hydrogen bonds : angle 4.87411 ( 2799) *********************** 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 37 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.066 Fit side-chains REVERT: A 431 TRP cc_start: 0.9230 (t60) cc_final: 0.8672 (t-100) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0297 time to fit residues: 1.6134 Evaluate side-chains 32 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 131 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 157 optimal weight: 0.0010 chunk 103 optimal weight: 50.0000 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 40.0000 chunk 166 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3235 r_free = 0.3235 target = 0.066043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052358 restraints weight = 18793.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.053298 restraints weight = 13906.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.053994 restraints weight = 11105.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054441 restraints weight = 9393.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054841 restraints weight = 8359.022| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5644 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= 0.133 Angle : 0.481 6.301 14752 Z= 0.266 Chirality : 0.040 0.119 1744 Planarity : 0.003 0.044 2004 Dihedral : 4.224 17.678 1808 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1708 helix: 1.96 (0.15), residues: 1080 sheet: -0.64 (0.30), residues: 268 loop : -1.61 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 56 TYR 0.009 0.001 TYR B 106 PHE 0.032 0.002 PHE C 291 TRP 0.023 0.002 TRP A 431 HIS 0.002 0.001 HIS D 438 Details of bonding type rmsd covalent geometry : bond 0.00226 (10676) covalent geometry : angle 0.48079 (14752) hydrogen bonds : bond 0.03299 ( 949) hydrogen bonds : angle 4.59351 ( 2799) *********************** REFINEMENT MACRO_CYCLE 7 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 : 0.102 Fit side-chains REVERT: D 72 MET cc_start: 0.9529 (ttt) cc_final: 0.8999 (ppp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0310 time to fit residues: 1.7027 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 : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 132 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 143 optimal weight: 0.0870 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 overall best weight: 2.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN D 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 = 0.3256 r_free = 0.3256 target = 0.066752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.053642 restraints weight = 20434.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054414 restraints weight = 15489.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055027 restraints weight = 12731.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055412 restraints weight = 11032.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.055737 restraints weight = 9964.561| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10676 Z= 0.128 Angle : 0.457 5.391 14752 Z= 0.257 Chirality : 0.040 0.130 1744 Planarity : 0.003 0.044 2004 Dihedral : 4.077 16.925 1808 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.20), residues: 1708 helix: 1.95 (0.15), residues: 1084 sheet: -0.55 (0.31), residues: 268 loop : -1.70 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 56 TYR 0.013 0.001 TYR C 426 PHE 0.025 0.001 PHE B 291 TRP 0.032 0.002 TRP B 431 HIS 0.002 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00224 (10676) covalent geometry : angle 0.45716 (14752) hydrogen bonds : bond 0.03116 ( 949) hydrogen bonds : angle 4.40032 ( 2799) *********************** REFINEMENT MACRO_CYCLE 8 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 : 0.095 Fit side-chains REVERT: D 72 MET cc_start: 0.9525 (ttt) cc_final: 0.8923 (ppp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0286 time to fit residues: 1.5833 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 118 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 41 optimal weight: 0.3980 chunk 13 optimal weight: 9.9990 chunk 143 optimal weight: 0.1980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3265 r_free = 0.3265 target = 0.067033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.053212 restraints weight = 19003.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054186 restraints weight = 13791.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.054905 restraints weight = 10964.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055409 restraints weight = 9221.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.055759 restraints weight = 8114.424| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10676 Z= 0.100 Angle : 0.437 5.333 14752 Z= 0.240 Chirality : 0.039 0.117 1744 Planarity : 0.003 0.044 2004 Dihedral : 3.877 17.064 1808 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.21), residues: 1708 helix: 2.20 (0.15), residues: 1092 sheet: -0.34 (0.31), residues: 268 loop : -1.43 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 56 TYR 0.008 0.001 TYR D 106 PHE 0.025 0.001 PHE D 452 TRP 0.032 0.002 TRP C 431 HIS 0.002 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00179 (10676) covalent geometry : angle 0.43746 (14752) hydrogen bonds : bond 0.02785 ( 949) hydrogen bonds : angle 4.15224 ( 2799) *********************** REFINEMENT MACRO_CYCLE 9 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 : 0.098 Fit side-chains REVERT: C 72 MET cc_start: 0.9589 (ttt) cc_final: 0.8914 (ppp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0287 time to fit residues: 1.6412 Evaluate side-chains 32 residues out of total 400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 110 optimal weight: 30.0000 chunk 118 optimal weight: 0.0010 chunk 16 optimal weight: 0.0000 chunk 30 optimal weight: 4.9990 chunk 147 optimal weight: 0.0030 chunk 29 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 114 optimal weight: 0.0170 chunk 62 optimal weight: 0.0670 chunk 70 optimal weight: 8.9990 overall best weight: 0.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN C 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 = 0.3301 r_free = 0.3301 target = 0.068661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.054365 restraints weight = 18089.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055425 restraints weight = 13076.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056125 restraints weight = 10294.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056715 restraints weight = 8681.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.057151 restraints weight = 7580.939| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10676 Z= 0.091 Angle : 0.435 5.509 14752 Z= 0.231 Chirality : 0.039 0.118 1744 Planarity : 0.003 0.046 2004 Dihedral : 3.654 15.753 1808 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1708 helix: 1.91 (0.15), residues: 1088 sheet: -0.09 (0.32), residues: 268 loop : -1.67 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 414 TYR 0.007 0.001 TYR B 123 PHE 0.029 0.001 PHE A 485 TRP 0.013 0.002 TRP A 475 HIS 0.004 0.001 HIS D 438 Details of bonding type rmsd covalent geometry : bond 0.00168 (10676) covalent geometry : angle 0.43488 (14752) hydrogen bonds : bond 0.02421 ( 949) hydrogen bonds : angle 3.93218 ( 2799) ********************** 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 : 0.137 Fit side-chains revert: symmetry clash REVERT: C 385 TRP cc_start: 0.9332 (m100) cc_final: 0.8700 (m-10) REVERT: C 452 PHE cc_start: 0.9379 (t80) cc_final: 0.9150 (t80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0330 time to fit residues: 1.8713 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 : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 117 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 140 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 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 = 0.3222 r_free = 0.3222 target = 0.064986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051266 restraints weight = 18918.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.052257 restraints weight = 13780.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052918 restraints weight = 10911.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053423 restraints weight = 9220.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.053634 restraints weight = 8117.300| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10676 Z= 0.186 Angle : 0.500 6.694 14752 Z= 0.287 Chirality : 0.040 0.161 1744 Planarity : 0.003 0.041 2004 Dihedral : 3.942 16.904 1808 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1708 helix: 1.74 (0.15), residues: 1088 sheet: -0.69 (0.31), residues: 268 loop : -1.61 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 255 TYR 0.013 0.001 TYR D 106 PHE 0.014 0.002 PHE C 485 TRP 0.010 0.002 TRP C 341 HIS 0.003 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00321 (10676) covalent geometry : angle 0.50007 (14752) hydrogen bonds : bond 0.03321 ( 949) hydrogen bonds : angle 4.41304 ( 2799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 929.23 seconds wall clock time: 16 minutes 47.03 seconds (1007.03 seconds total)