Starting phenix.real_space_refine on Wed Sep 25 12:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/09_2024/6ayg_7020.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/09_2024/6ayg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/09_2024/6ayg_7020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/09_2024/6ayg_7020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/09_2024/6ayg_7020.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/09_2024/6ayg_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-5461/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: 4.92, per 1000 atoms: 0.47 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 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: 1.11 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: 3.09 Time building geometry restraints manager: 3.36 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: 0.00 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: 0.370 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.750 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.1163 time to fit residues: 7.0597 Evaluate side-chains 39 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 D 252 PHE 0.020 0.002 PHE D 489 TYR 0.019 0.003 TYR B 481 ARG 0.005 0.001 ARG D 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 fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9236 (tp-100) cc_final: 0.8921 (tp-100) REVERT: A 385 TRP cc_start: 0.9206 (m100) cc_final: 0.8837 (m-90) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1010 time to fit residues: 6.3565 Evaluate side-chains 39 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 106 optimal weight: 0.7980 chunk 43 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 139 optimal weight: 0.0770 chunk 155 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 overall best weight: 3.5744 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10676 Z= 0.184 Angle : 0.506 5.827 14752 Z= 0.296 Chirality : 0.040 0.117 1744 Planarity : 0.004 0.051 2004 Dihedral : 4.924 19.311 1808 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % 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: -0.38 (0.19), residues: 1708 helix: 0.63 (0.15), residues: 1056 sheet: -0.86 (0.30), residues: 232 loop : -1.96 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 431 HIS 0.003 0.001 HIS C 252 PHE 0.028 0.002 PHE A 489 TYR 0.011 0.001 TYR A 123 ARG 0.002 0.000 ARG A 479 *********************** 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 fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.254 Fit side-chains REVERT: A 76 GLN cc_start: 0.9281 (tp-100) cc_final: 0.9016 (tp-100) REVERT: A 255 ARG cc_start: 0.8149 (ptt180) cc_final: 0.7060 (mmt90) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0925 time to fit residues: 5.4885 Evaluate side-chains 36 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 40.0000 chunk 117 optimal weight: 0.0170 chunk 81 optimal weight: 30.0000 chunk 17 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 105 optimal weight: 0.0870 chunk 157 optimal weight: 0.0670 chunk 166 optimal weight: 0.0170 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 0.0050 chunk 44 optimal weight: 0.8980 overall best weight: 0.0386 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4881 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= 0.127 Angle : 0.472 7.077 14752 Z= 0.260 Chirality : 0.039 0.118 1744 Planarity : 0.003 0.050 2004 Dihedral : 4.416 19.665 1808 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 0.93 (0.20), residues: 1708 helix: 1.70 (0.15), residues: 1076 sheet: -0.36 (0.29), residues: 268 loop : -1.89 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 385 HIS 0.003 0.001 HIS A 252 PHE 0.015 0.001 PHE B 291 TYR 0.011 0.001 TYR D 481 ARG 0.002 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 47 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.9599 (ttm) cc_final: 0.9240 (ttt) REVERT: A 76 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8884 (tp-100) REVERT: A 255 ARG cc_start: 0.7935 (ptt180) cc_final: 0.7161 (tpp-160) REVERT: A 385 TRP cc_start: 0.8984 (m100) cc_final: 0.8395 (m-10) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0931 time to fit residues: 5.7506 Evaluate side-chains 41 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 30.0000 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 0.0010 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 1.3190 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5252 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= 0.127 Angle : 0.435 6.252 14752 Z= 0.244 Chirality : 0.039 0.175 1744 Planarity : 0.003 0.048 2004 Dihedral : 4.139 18.171 1808 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 1.62 (0.20), residues: 1708 helix: 2.23 (0.16), residues: 1076 sheet: -0.06 (0.29), residues: 272 loop : -1.63 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 385 HIS 0.001 0.000 HIS C 100 PHE 0.020 0.001 PHE C 489 TYR 0.008 0.001 TYR D 123 ARG 0.001 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 48 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.288 Fit side-chains REVERT: A 72 MET cc_start: 0.9568 (ttm) cc_final: 0.9274 (ttt) REVERT: A 255 ARG cc_start: 0.7635 (ptt180) cc_final: 0.7180 (tpp-160) REVERT: A 385 TRP cc_start: 0.8995 (m100) cc_final: 0.8390 (m-10) REVERT: A 405 LEU cc_start: 0.9095 (tp) cc_final: 0.8830 (pp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0947 time to fit residues: 5.9629 Evaluate side-chains 37 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 97 optimal weight: 40.0000 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 160 optimal weight: 0.4980 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10676 Z= 0.158 Angle : 0.464 6.484 14752 Z= 0.260 Chirality : 0.039 0.137 1744 Planarity : 0.003 0.047 2004 Dihedral : 4.020 16.208 1808 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.58 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 (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: 1.93 (0.21), residues: 1708 helix: 2.50 (0.16), residues: 1072 sheet: 0.04 (0.29), residues: 272 loop : -1.59 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 431 HIS 0.002 0.001 HIS C 100 PHE 0.020 0.002 PHE B 452 TYR 0.006 0.001 TYR A 123 ARG 0.001 0.000 ARG D 56 *********************** 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 42 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.313 Fit side-chains REVERT: A 72 MET cc_start: 0.9592 (ttm) cc_final: 0.9292 (ttt) REVERT: A 385 TRP cc_start: 0.9006 (m100) cc_final: 0.8414 (m-10) REVERT: A 405 LEU cc_start: 0.9094 (tp) cc_final: 0.8788 (pp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0766 time to fit residues: 4.5870 Evaluate side-chains 35 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 103 optimal weight: 50.0000 chunk 101 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 66 optimal weight: 7.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10676 Z= 0.160 Angle : 0.457 6.134 14752 Z= 0.261 Chirality : 0.040 0.139 1744 Planarity : 0.003 0.045 2004 Dihedral : 4.013 18.689 1808 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 2.10 (0.21), residues: 1708 helix: 2.67 (0.16), residues: 1072 sheet: -0.07 (0.29), residues: 272 loop : -1.47 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 385 HIS 0.002 0.001 HIS C 100 PHE 0.015 0.002 PHE C 452 TYR 0.027 0.001 TYR D 426 ARG 0.001 0.000 ARG C 255 *********************** 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 42 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.266 Fit side-chains REVERT: A 72 MET cc_start: 0.9624 (ttm) cc_final: 0.9314 (ttp) REVERT: A 385 TRP cc_start: 0.9038 (m100) cc_final: 0.8448 (m-10) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0758 time to fit residues: 4.6231 Evaluate side-chains 35 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 105 optimal weight: 0.0040 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 130 optimal weight: 0.0060 chunk 150 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 overall best weight: 3.8014 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5852 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= 0.175 Angle : 0.462 6.194 14752 Z= 0.262 Chirality : 0.039 0.118 1744 Planarity : 0.003 0.043 2004 Dihedral : 3.958 16.288 1808 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.74 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: 2.04 (0.21), residues: 1708 helix: 2.60 (0.16), residues: 1092 sheet: -0.23 (0.29), residues: 272 loop : -1.52 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 385 HIS 0.002 0.001 HIS A 100 PHE 0.022 0.002 PHE B 452 TYR 0.011 0.001 TYR D 106 ARG 0.001 0.000 ARG D 479 *********************** 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 40 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.267 Fit side-chains REVERT: C 72 MET cc_start: 0.9633 (ttm) cc_final: 0.9330 (ttp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0750 time to fit residues: 4.2552 Evaluate side-chains 33 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 30.0000 chunk 158 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 67 optimal weight: 30.0000 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 146 optimal weight: 50.0000 chunk 153 optimal weight: 40.0000 chunk 101 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10676 Z= 0.304 Angle : 0.559 8.145 14752 Z= 0.332 Chirality : 0.041 0.185 1744 Planarity : 0.004 0.045 2004 Dihedral : 4.537 22.147 1808 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: 0.83 (0.20), residues: 1708 helix: 1.64 (0.16), residues: 1080 sheet: -0.48 (0.30), residues: 264 loop : -1.94 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 431 HIS 0.004 0.001 HIS C 100 PHE 0.020 0.003 PHE D 485 TYR 0.021 0.002 TYR B 426 ARG 0.002 0.001 ARG D 414 *********************** 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 36 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.269 Fit side-chains REVERT: A 72 MET cc_start: 0.9653 (ttm) cc_final: 0.9364 (ttt) REVERT: A 385 TRP cc_start: 0.9161 (m100) cc_final: 0.8694 (m-10) REVERT: A 405 LEU cc_start: 0.9093 (mm) cc_final: 0.8829 (mm) REVERT: A 431 TRP cc_start: 0.9167 (t60) cc_final: 0.8728 (t-100) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0704 time to fit residues: 3.6783 Evaluate side-chains 32 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 157 optimal weight: 0.0030 chunk 136 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 145 optimal weight: 0.0770 overall best weight: 0.4350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6299 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= 0.121 Angle : 0.471 6.397 14752 Z= 0.251 Chirality : 0.039 0.116 1744 Planarity : 0.003 0.047 2004 Dihedral : 3.963 22.030 1808 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: 1.72 (0.21), residues: 1708 helix: 2.37 (0.15), residues: 1096 sheet: -0.32 (0.31), residues: 268 loop : -1.77 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 431 HIS 0.002 0.001 HIS B 438 PHE 0.025 0.002 PHE A 80 TYR 0.007 0.001 TYR D 481 ARG 0.002 0.001 ARG B 414 ********************** REFINEMENT MACRO_CYCLE 10 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 41 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.271 Fit side-chains REVERT: C 72 MET cc_start: 0.9629 (ttm) cc_final: 0.9315 (ttp) REVERT: C 385 TRP cc_start: 0.9069 (m100) cc_final: 0.8477 (m-10) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0727 time to fit residues: 4.2330 Evaluate side-chains 34 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 140 optimal weight: 30.0000 chunk 17 optimal weight: 50.0000 chunk 25 optimal weight: 30.0000 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.066000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.052027 restraints weight = 18354.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053022 restraints weight = 13298.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053773 restraints weight = 10443.086| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6368 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= 0.144 Angle : 0.426 5.092 14752 Z= 0.242 Chirality : 0.039 0.118 1744 Planarity : 0.003 0.044 2004 Dihedral : 3.807 16.095 1808 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 1.80 (0.21), residues: 1708 helix: 2.44 (0.15), residues: 1088 sheet: -0.29 (0.31), residues: 272 loop : -1.69 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 385 HIS 0.002 0.001 HIS C 438 PHE 0.015 0.001 PHE B 485 TYR 0.008 0.001 TYR D 106 ARG 0.001 0.000 ARG B 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1393.62 seconds wall clock time: 25 minutes 33.23 seconds (1533.23 seconds total)