Starting phenix.real_space_refine on Fri Jul 3 08:06:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tw2_26148/07_2026/7tw2_26148.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tw2_26148/07_2026/7tw2_26148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tw2_26148/07_2026/7tw2_26148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tw2_26148/07_2026/7tw2_26148.map" model { file = "/net/cci-nas-00/data/ceres_data/7tw2_26148/07_2026/7tw2_26148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tw2_26148/07_2026/7tw2_26148.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tw2_26148/07_2026/7tw2_26148.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tw2_26148/07_2026/7tw2_26148.cif" } resolution = 4.8 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= 0.000 sd= 0.002 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 48 5.16 5 C 8429 2.51 5 N 2122 2.21 5 O 2239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12838 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6435 Classifications: {'peptide': 814} Link IDs: {'PTRANS': 49, 'TRANS': 764} Chain breaks: 3 Chain: "A" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6375 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 47, 'TRANS': 757} Chain breaks: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.20 Number of scatterers: 12838 At special positions: 0 Unit cell: (120.006, 96.642, 147.618, 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 48 16.00 O 2239 8.00 N 2122 7.00 C 8429 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 Links applied NAG-ASN " NAG A1000 " - " ASN A 642 " " NAG B1000 " - " ASN B 642 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 475.4 milliseconds 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 8 sheets defined 61.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 103 through 116 removed outlier: 4.084A pdb=" N LYS B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 142 Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.975A pdb=" N ARG B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 277 through 291 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 317 removed outlier: 4.265A pdb=" N LEU B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 335 through 349 removed outlier: 4.116A pdb=" N SER B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 390 Processing helix chain 'B' and resid 392 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 4.062A pdb=" N LEU B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 removed outlier: 3.684A pdb=" N LEU B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.622A pdb=" N LEU B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 507 removed outlier: 3.667A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 517 through 547 removed outlier: 3.615A pdb=" N GLN B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.976A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.529A pdb=" N ILE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 removed outlier: 3.734A pdb=" N ALA B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 719 Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.597A pdb=" N LEU B 764 " --> pdb=" O ARG B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 786 through 799 removed outlier: 3.987A pdb=" N GLY B 790 " --> pdb=" O ALA B 786 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 791 " --> pdb=" O VAL B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 811 removed outlier: 3.675A pdb=" N ASP B 807 " --> pdb=" O ILE B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 removed outlier: 3.580A pdb=" N LYS B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 858 through 865 removed outlier: 3.698A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 removed outlier: 3.617A pdb=" N LEU B 869 " --> pdb=" O LEU B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 879 through 887 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.826A pdb=" N GLU A 168 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.507A pdb=" N GLN A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 277 through 291 removed outlier: 3.578A pdb=" N GLU A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 303 through 317 removed outlier: 4.025A pdb=" N LEU A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 335 through 347 Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.553A pdb=" N VAL A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 4.016A pdb=" N LEU A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 removed outlier: 3.731A pdb=" N LEU A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.574A pdb=" N LEU A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 removed outlier: 3.706A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 517 through 547 removed outlier: 3.662A pdb=" N GLN A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.862A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 removed outlier: 3.522A pdb=" N PHE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.530A pdb=" N MET A 664 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.635A pdb=" N ALA A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.832A pdb=" N LYS A 695 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 786 through 799 removed outlier: 3.980A pdb=" N GLY A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 791 " --> pdb=" O VAL A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.579A pdb=" N ASP A 807 " --> pdb=" O ILE A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.784A pdb=" N LYS A 826 " --> pdb=" O VAL A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 853 removed outlier: 3.635A pdb=" N LEU A 835 " --> pdb=" O TRP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 858 through 872 removed outlier: 3.947A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 67 removed outlier: 6.585A pdb=" N VAL B 59 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 80 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU B 61 " --> pdb=" O ALA B 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 87 current: chain 'B' and resid 226 through 234 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 226 through 234 current: chain 'B' and resid 262 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.620A pdb=" N LEU B 319 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 319 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 740 Processing sheet with id=AA5, first strand: chain 'A' and resid 56 through 67 removed outlier: 7.025A pdb=" N VAL A 59 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A 61 " --> pdb=" O ALA A 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 86 through 87 current: chain 'A' and resid 262 through 269 Processing sheet with id=AA6, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA7, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.747A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1950 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: 1.78 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4038 1.34 - 1.46: 2842 1.46 - 1.58: 6176 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 13142 Sorted by residual: bond pdb=" N LEU B 706 " pdb=" CA LEU B 706 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.91e+00 bond pdb=" N TRP B 662 " pdb=" CA TRP B 662 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.23e-02 6.61e+03 4.62e+00 bond pdb=" C1 NAG B1000 " pdb=" O5 NAG B1000 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C1 NAG A1000 " pdb=" O5 NAG A1000 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" C VAL A 560 " pdb=" N PRO A 561 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.66e+00 ... (remaining 13137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 17429 2.05 - 4.11: 347 4.11 - 6.16: 55 6.16 - 8.22: 20 8.22 - 10.27: 8 Bond angle restraints: 17859 Sorted by residual: angle pdb=" N TRP B 662 " pdb=" CA TRP B 662 " pdb=" C TRP B 662 " ideal model delta sigma weight residual 111.36 107.14 4.22 1.09e+00 8.42e-01 1.50e+01 angle pdb=" N LYS A 695 " pdb=" CA LYS A 695 " pdb=" C LYS A 695 " ideal model delta sigma weight residual 111.30 116.42 -5.12 1.36e+00 5.41e-01 1.42e+01 angle pdb=" CB MET B 586 " pdb=" CG MET B 586 " pdb=" SD MET B 586 " ideal model delta sigma weight residual 112.70 122.94 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CA GLU B 254 " pdb=" CB GLU B 254 " pdb=" CG GLU B 254 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET B 712 " pdb=" CG MET B 712 " pdb=" SD MET B 712 " ideal model delta sigma weight residual 112.70 122.19 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 17854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7146 17.95 - 35.91: 573 35.91 - 53.86: 88 53.86 - 71.81: 12 71.81 - 89.76: 18 Dihedral angle restraints: 7837 sinusoidal: 3160 harmonic: 4677 Sorted by residual: dihedral pdb=" CA TRP B 81 " pdb=" C TRP B 81 " pdb=" N VAL B 82 " pdb=" CA VAL B 82 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TYR A 555 " pdb=" C TYR A 555 " pdb=" N ASN A 556 " pdb=" CA ASN A 556 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TYR B 555 " pdb=" C TYR B 555 " pdb=" N ASN B 556 " pdb=" CA ASN B 556 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1722 0.057 - 0.113: 332 0.113 - 0.170: 38 0.170 - 0.226: 2 0.226 - 0.283: 1 Chirality restraints: 2095 Sorted by residual: chirality pdb=" CA MET B 300 " pdb=" N MET B 300 " pdb=" C MET B 300 " pdb=" CB MET B 300 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA LYS A 219 " pdb=" N LYS A 219 " pdb=" C LYS A 219 " pdb=" CB LYS A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE B 296 " pdb=" CA ILE B 296 " pdb=" CG1 ILE B 296 " pdb=" CG2 ILE B 296 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.37e-01 ... (remaining 2092 not shown) Planarity restraints: 2242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 447 " -0.023 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" C GLN B 447 " 0.080 2.00e-02 2.50e+03 pdb=" O GLN B 447 " -0.030 2.00e-02 2.50e+03 pdb=" N GLY B 448 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 831 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C TRP B 831 " 0.077 2.00e-02 2.50e+03 pdb=" O TRP B 831 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG B 832 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 197 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C THR A 197 " 0.057 2.00e-02 2.50e+03 pdb=" O THR A 197 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 198 " -0.019 2.00e-02 2.50e+03 ... (remaining 2239 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 611 2.72 - 3.27: 12954 3.27 - 3.81: 20545 3.81 - 4.36: 24058 4.36 - 4.90: 41847 Nonbonded interactions: 100015 Sorted by model distance: nonbonded pdb=" OE2 GLU B 63 " pdb=" OG1 THR B 279 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG A 646 " pdb=" O GLY A 647 " model vdw 2.207 3.120 nonbonded pdb=" ND2 ASN B 569 " pdb=" O PRO A 568 " model vdw 2.216 3.120 nonbonded pdb=" OE2 GLU B 291 " pdb=" NE ARG B 346 " model vdw 2.257 3.120 nonbonded pdb=" NH1 ARG B 646 " pdb=" O GLY B 647 " model vdw 2.260 3.120 ... (remaining 100010 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' and (resid 55 through 348 or resid 369 through 1000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.003 0.030 13144 Z= 0.143 Angle : 0.749 10.273 17865 Z= 0.377 Chirality : 0.043 0.283 2095 Planarity : 0.005 0.058 2240 Dihedral : 13.684 89.764 4807 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.72 % 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: -1.27 (0.19), residues: 1603 helix: 0.08 (0.17), residues: 903 sheet: -0.26 (0.54), residues: 85 loop : -2.33 (0.20), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 387 TYR 0.033 0.002 TYR B 58 PHE 0.022 0.001 PHE B 244 TRP 0.013 0.001 TRP B 492 HIS 0.004 0.001 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (13142) covalent geometry : angle 0.74943 / 0.38 (17859) hydrogen bonds : bond 0.13588 / 9.19 ( 670) hydrogen bonds : angle 5.20485 / 3.54 ( 1950) link_NAG-ASN : bond 0.00176 / 0.08 ( 2) link_NAG-ASN : angle 0.83533 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 MET cc_start: 0.9141 (tmm) cc_final: 0.8731 (tmm) REVERT: B 776 MET cc_start: 0.8765 (mpp) cc_final: 0.8464 (mpp) REVERT: A 264 PHE cc_start: 0.7663 (m-80) cc_final: 0.7022 (m-80) REVERT: A 741 MET cc_start: 0.7191 (mtp) cc_final: 0.6716 (mtp) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.0825 time to fit residues: 10.8813 Evaluate side-chains 57 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 87 ASN B 569 ASN B 651 HIS A 87 ASN A 569 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.070852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.048837 restraints weight = 131632.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.049635 restraints weight = 78134.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.050086 restraints weight = 50369.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.050326 restraints weight = 36314.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.051007 restraints weight = 27197.738| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13144 Z= 0.143 Angle : 0.584 6.600 17865 Z= 0.282 Chirality : 0.039 0.142 2095 Planarity : 0.005 0.051 2240 Dihedral : 3.814 20.971 1735 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: 0.42 (0.21), residues: 1603 helix: 1.39 (0.17), residues: 925 sheet: 0.35 (0.59), residues: 81 loop : -1.54 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 760 TYR 0.017 0.002 TYR B 58 PHE 0.017 0.001 PHE A 471 TRP 0.010 0.001 TRP B 492 HIS 0.004 0.001 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (13142) covalent geometry : angle 0.58419 / 0.28 (17859) hydrogen bonds : bond 0.03703 / 2.49 ( 670) hydrogen bonds : angle 4.06294 / 2.87 ( 1950) link_NAG-ASN : bond 0.00452 / 0.22 ( 2) link_NAG-ASN : angle 1.03112 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.343 Fit side-chains REVERT: B 578 MET cc_start: 0.9189 (tmm) cc_final: 0.8764 (tmm) REVERT: A 471 PHE cc_start: 0.9666 (t80) cc_final: 0.9365 (t80) REVERT: A 498 ILE cc_start: 0.9796 (mm) cc_final: 0.9593 (pt) REVERT: A 741 MET cc_start: 0.7519 (mtp) cc_final: 0.7047 (mtp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0869 time to fit residues: 9.8030 Evaluate side-chains 51 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 86 optimal weight: 30.0000 chunk 144 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 8 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 133 ASN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.067764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.046697 restraints weight = 134745.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.047496 restraints weight = 81968.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.047946 restraints weight = 51745.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.048367 restraints weight = 37423.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.048600 restraints weight = 28946.523| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13144 Z= 0.209 Angle : 0.672 7.990 17865 Z= 0.330 Chirality : 0.041 0.166 2095 Planarity : 0.005 0.044 2240 Dihedral : 4.161 24.005 1735 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % 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: 0.65 (0.21), residues: 1603 helix: 1.38 (0.17), residues: 935 sheet: 0.02 (0.57), residues: 81 loop : -1.05 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 760 TYR 0.016 0.002 TYR B 278 PHE 0.021 0.002 PHE A 544 TRP 0.035 0.002 TRP B 662 HIS 0.005 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (13142) covalent geometry : angle 0.67101 / 0.33 (17859) hydrogen bonds : bond 0.03985 / 2.66 ( 670) hydrogen bonds : angle 4.38587 / 3.09 ( 1950) link_NAG-ASN : bond 0.00400 / 0.20 ( 2) link_NAG-ASN : angle 1.93905 / 1.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 578 MET cc_start: 0.9058 (tmm) cc_final: 0.8588 (tmm) REVERT: B 696 MET cc_start: 0.8352 (mtm) cc_final: 0.8045 (mpp) REVERT: B 861 PHE cc_start: 0.9467 (t80) cc_final: 0.9220 (t80) REVERT: A 471 PHE cc_start: 0.9672 (t80) cc_final: 0.9348 (t80) REVERT: A 663 MET cc_start: 0.9464 (tpt) cc_final: 0.9229 (tpt) REVERT: A 741 MET cc_start: 0.7460 (mtp) cc_final: 0.7022 (mtp) REVERT: A 833 MET cc_start: 0.9101 (ptp) cc_final: 0.8255 (ptp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0794 time to fit residues: 8.6356 Evaluate side-chains 51 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 33 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 433 ASN A 163 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.068483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.047298 restraints weight = 133546.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.048188 restraints weight = 80690.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.048694 restraints weight = 50988.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.049212 restraints weight = 36393.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.049392 restraints weight = 27729.331| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13144 Z= 0.155 Angle : 0.589 7.385 17865 Z= 0.285 Chirality : 0.040 0.161 2095 Planarity : 0.004 0.041 2240 Dihedral : 4.029 21.000 1735 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 0.96 (0.21), residues: 1603 helix: 1.61 (0.17), residues: 947 sheet: -0.21 (0.57), residues: 82 loop : -0.87 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 389 TYR 0.017 0.002 TYR B 278 PHE 0.036 0.002 PHE B 266 TRP 0.029 0.002 TRP B 662 HIS 0.009 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (13142) covalent geometry : angle 0.58835 / 0.29 (17859) hydrogen bonds : bond 0.03647 / 2.47 ( 670) hydrogen bonds : angle 4.19327 / 2.96 ( 1950) link_NAG-ASN : bond 0.00310 / 0.15 ( 2) link_NAG-ASN : angle 1.77563 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: B 559 MET cc_start: 0.8719 (tpp) cc_final: 0.8143 (tpp) REVERT: B 578 MET cc_start: 0.9076 (tmm) cc_final: 0.8779 (tmm) REVERT: B 861 PHE cc_start: 0.9455 (t80) cc_final: 0.9195 (t80) REVERT: A 471 PHE cc_start: 0.9667 (t80) cc_final: 0.9392 (t80) REVERT: A 675 PHE cc_start: 0.9233 (t80) cc_final: 0.8859 (t80) REVERT: A 741 MET cc_start: 0.7451 (mtp) cc_final: 0.7200 (mtp) REVERT: A 833 MET cc_start: 0.9048 (ptp) cc_final: 0.8252 (ptp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0862 time to fit residues: 9.3337 Evaluate side-chains 52 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 57 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 20.0000 chunk 151 optimal weight: 1.9990 chunk 3 optimal weight: 30.0000 chunk 64 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.067780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.046572 restraints weight = 132114.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.047147 restraints weight = 80280.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.047761 restraints weight = 54503.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.048351 restraints weight = 37988.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.048391 restraints weight = 29062.438| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13144 Z= 0.166 Angle : 0.608 7.106 17865 Z= 0.294 Chirality : 0.040 0.165 2095 Planarity : 0.004 0.040 2240 Dihedral : 4.122 23.537 1735 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 1.11 (0.21), residues: 1603 helix: 1.69 (0.17), residues: 946 sheet: -0.42 (0.57), residues: 82 loop : -0.67 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 389 TYR 0.017 0.002 TYR B 278 PHE 0.016 0.001 PHE A 836 TRP 0.027 0.002 TRP B 662 HIS 0.004 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (13142) covalent geometry : angle 0.60684 / 0.29 (17859) hydrogen bonds : bond 0.03642 / 2.45 ( 670) hydrogen bonds : angle 4.21555 / 2.98 ( 1950) link_NAG-ASN : bond 0.00318 / 0.15 ( 2) link_NAG-ASN : angle 1.90264 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 559 MET cc_start: 0.8604 (tpp) cc_final: 0.8257 (tpp) REVERT: B 578 MET cc_start: 0.9085 (tmm) cc_final: 0.8784 (tmm) REVERT: B 696 MET cc_start: 0.8473 (mtp) cc_final: 0.7958 (mpp) REVERT: B 861 PHE cc_start: 0.9321 (t80) cc_final: 0.9061 (t80) REVERT: A 471 PHE cc_start: 0.9591 (t80) cc_final: 0.9303 (t80) REVERT: A 833 MET cc_start: 0.9033 (ptp) cc_final: 0.8281 (ptp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0715 time to fit residues: 7.3772 Evaluate side-chains 51 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 23 optimal weight: 5.9990 chunk 153 optimal weight: 0.0570 chunk 82 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 26 optimal weight: 0.0870 chunk 157 optimal weight: 0.0050 chunk 60 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 840 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.069804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.049274 restraints weight = 132298.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.049710 restraints weight = 81549.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.050289 restraints weight = 52362.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.050936 restraints weight = 36160.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.051076 restraints weight = 27394.150| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13144 Z= 0.097 Angle : 0.551 6.946 17865 Z= 0.257 Chirality : 0.039 0.172 2095 Planarity : 0.004 0.042 2240 Dihedral : 3.845 21.945 1735 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 1.49 (0.21), residues: 1603 helix: 2.01 (0.17), residues: 944 sheet: -0.14 (0.57), residues: 82 loop : -0.55 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 389 TYR 0.013 0.001 TYR B 278 PHE 0.015 0.001 PHE A 836 TRP 0.028 0.001 TRP B 662 HIS 0.005 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (13142) covalent geometry : angle 0.55059 / 0.26 (17859) hydrogen bonds : bond 0.03307 / 2.24 ( 670) hydrogen bonds : angle 3.91982 / 2.77 ( 1950) link_NAG-ASN : bond 0.00316 / 0.15 ( 2) link_NAG-ASN : angle 1.21645 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 559 MET cc_start: 0.8659 (tpp) cc_final: 0.8307 (tpp) REVERT: B 578 MET cc_start: 0.9013 (tmm) cc_final: 0.8724 (tmm) REVERT: B 696 MET cc_start: 0.8470 (mtp) cc_final: 0.8052 (mpp) REVERT: B 776 MET cc_start: 0.8902 (mpp) cc_final: 0.8590 (mpp) REVERT: B 861 PHE cc_start: 0.9350 (t80) cc_final: 0.9056 (t80) REVERT: A 471 PHE cc_start: 0.9673 (t80) cc_final: 0.9386 (t80) REVERT: A 675 PHE cc_start: 0.9216 (t80) cc_final: 0.8876 (t80) REVERT: A 833 MET cc_start: 0.9026 (ptp) cc_final: 0.8233 (ptp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0848 time to fit residues: 9.2285 Evaluate side-chains 52 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 38 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 48 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 434 GLN ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN A 547 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.065470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.044963 restraints weight = 132588.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.045783 restraints weight = 81517.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.046080 restraints weight = 51835.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.046616 restraints weight = 39226.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.046845 restraints weight = 31406.629| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13144 Z= 0.317 Angle : 0.822 11.619 17865 Z= 0.410 Chirality : 0.045 0.203 2095 Planarity : 0.006 0.066 2240 Dihedral : 4.715 23.506 1735 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 0.47 (0.20), residues: 1603 helix: 1.04 (0.17), residues: 941 sheet: -0.46 (0.56), residues: 83 loop : -0.69 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 808 TYR 0.020 0.003 TYR B 278 PHE 0.026 0.003 PHE A 464 TRP 0.027 0.003 TRP B 662 HIS 0.007 0.002 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.32 (13142) covalent geometry : angle 0.81986 / 0.41 (17859) hydrogen bonds : bond 0.04480 / 3.01 ( 670) hydrogen bonds : angle 4.87168 / 3.43 ( 1950) link_NAG-ASN : bond 0.00133 / 0.06 ( 2) link_NAG-ASN : angle 2.99410 / 2.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 559 MET cc_start: 0.8777 (tpp) cc_final: 0.8516 (tpp) REVERT: B 578 MET cc_start: 0.9050 (tmm) cc_final: 0.8760 (tmm) REVERT: B 861 PHE cc_start: 0.9387 (t80) cc_final: 0.9118 (t80) REVERT: A 471 PHE cc_start: 0.9620 (t80) cc_final: 0.9326 (t80) REVERT: A 663 MET cc_start: 0.9367 (tpt) cc_final: 0.9103 (tpt) REVERT: A 696 MET cc_start: 0.8724 (pmm) cc_final: 0.8512 (pmm) REVERT: A 833 MET cc_start: 0.9203 (ptp) cc_final: 0.8993 (ptp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0829 time to fit residues: 8.6447 Evaluate side-chains 49 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 50.0000 chunk 97 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 148 optimal weight: 0.0570 chunk 109 optimal weight: 9.9990 overall best weight: 2.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.067999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.047251 restraints weight = 132376.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.047977 restraints weight = 79941.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.048360 restraints weight = 50870.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.048910 restraints weight = 36104.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.048981 restraints weight = 27414.829| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13144 Z= 0.122 Angle : 0.613 9.961 17865 Z= 0.290 Chirality : 0.040 0.180 2095 Planarity : 0.004 0.053 2240 Dihedral : 4.260 23.491 1735 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 1.19 (0.21), residues: 1603 helix: 1.69 (0.17), residues: 940 sheet: -0.22 (0.57), residues: 82 loop : -0.50 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 295 TYR 0.017 0.001 TYR B 278 PHE 0.020 0.001 PHE B 659 TRP 0.067 0.002 TRP B 662 HIS 0.005 0.001 HIS B 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13142) covalent geometry : angle 0.61246 / 0.29 (17859) hydrogen bonds : bond 0.03654 / 2.46 ( 670) hydrogen bonds : angle 4.25488 / 3.01 ( 1950) link_NAG-ASN : bond 0.00291 / 0.14 ( 2) link_NAG-ASN : angle 1.97954 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 559 MET cc_start: 0.8434 (tpp) cc_final: 0.8192 (tpp) REVERT: B 578 MET cc_start: 0.9058 (tmm) cc_final: 0.8777 (tmm) REVERT: B 696 MET cc_start: 0.8472 (mtp) cc_final: 0.8015 (mpp) REVERT: B 776 MET cc_start: 0.8789 (mpp) cc_final: 0.8537 (mpp) REVERT: B 861 PHE cc_start: 0.9306 (t80) cc_final: 0.9040 (t80) REVERT: A 663 MET cc_start: 0.9416 (tpt) cc_final: 0.9118 (tpt) REVERT: A 675 PHE cc_start: 0.9067 (t80) cc_final: 0.8795 (t80) REVERT: A 795 MET cc_start: 0.8979 (mtm) cc_final: 0.8731 (mtm) REVERT: A 833 MET cc_start: 0.9134 (ptp) cc_final: 0.8881 (ptp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0852 time to fit residues: 9.1060 Evaluate side-chains 49 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 40.0000 chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 50.0000 chunk 154 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.066647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.046838 restraints weight = 129801.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.047424 restraints weight = 79933.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.048005 restraints weight = 50747.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.048265 restraints weight = 35961.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.048689 restraints weight = 28575.569| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13144 Z= 0.174 Angle : 0.653 9.966 17865 Z= 0.314 Chirality : 0.041 0.170 2095 Planarity : 0.005 0.050 2240 Dihedral : 4.313 23.858 1735 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 1.11 (0.21), residues: 1603 helix: 1.61 (0.17), residues: 935 sheet: -0.27 (0.58), residues: 82 loop : -0.49 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 295 TYR 0.017 0.002 TYR B 278 PHE 0.022 0.002 PHE A 836 TRP 0.063 0.002 TRP B 662 HIS 0.005 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (13142) covalent geometry : angle 0.65216 / 0.31 (17859) hydrogen bonds : bond 0.03735 / 2.51 ( 670) hydrogen bonds : angle 4.37634 / 3.10 ( 1950) link_NAG-ASN : bond 0.00305 / 0.15 ( 2) link_NAG-ASN : angle 1.59566 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: B 559 MET cc_start: 0.8539 (tpp) cc_final: 0.8236 (tpp) REVERT: B 578 MET cc_start: 0.9071 (tmm) cc_final: 0.8772 (tmm) REVERT: B 696 MET cc_start: 0.8521 (mtp) cc_final: 0.8070 (mpp) REVERT: B 776 MET cc_start: 0.8870 (mpp) cc_final: 0.8599 (mpp) REVERT: B 861 PHE cc_start: 0.9365 (t80) cc_final: 0.9129 (t80) REVERT: A 663 MET cc_start: 0.9453 (tpt) cc_final: 0.9203 (tpt) REVERT: A 696 MET cc_start: 0.8583 (pmm) cc_final: 0.8342 (pmm) REVERT: A 741 MET cc_start: 0.7052 (mmm) cc_final: 0.6760 (mmm) REVERT: A 795 MET cc_start: 0.9015 (mtm) cc_final: 0.8766 (mtm) REVERT: A 833 MET cc_start: 0.9171 (ptp) cc_final: 0.8908 (ptp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0795 time to fit residues: 8.2786 Evaluate side-chains 51 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 151 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.067577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.047286 restraints weight = 132511.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.048092 restraints weight = 79589.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.048533 restraints weight = 49990.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.049075 restraints weight = 35371.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.049147 restraints weight = 25690.340| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13144 Z= 0.128 Angle : 0.603 10.118 17865 Z= 0.286 Chirality : 0.040 0.174 2095 Planarity : 0.004 0.047 2240 Dihedral : 4.167 23.252 1735 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 1.36 (0.21), residues: 1603 helix: 1.84 (0.17), residues: 935 sheet: -0.06 (0.59), residues: 80 loop : -0.45 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 295 TYR 0.016 0.001 TYR B 278 PHE 0.021 0.001 PHE A 836 TRP 0.060 0.002 TRP B 662 HIS 0.004 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13142) covalent geometry : angle 0.60207 / 0.29 (17859) hydrogen bonds : bond 0.03457 / 2.33 ( 670) hydrogen bonds : angle 4.19100 / 2.97 ( 1950) link_NAG-ASN : bond 0.00337 / 0.16 ( 2) link_NAG-ASN : angle 1.40556 / 1.02 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3206 Ramachandran restraints generated. 1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: B 559 MET cc_start: 0.8331 (tpp) cc_final: 0.7986 (tpp) REVERT: B 578 MET cc_start: 0.9067 (tmm) cc_final: 0.8789 (tmm) REVERT: B 696 MET cc_start: 0.8526 (mtp) cc_final: 0.8086 (mpp) REVERT: B 721 MET cc_start: 0.8717 (mpp) cc_final: 0.7958 (mtm) REVERT: B 776 MET cc_start: 0.8866 (mpp) cc_final: 0.8597 (mpp) REVERT: B 861 PHE cc_start: 0.9316 (t80) cc_final: 0.9098 (t80) REVERT: A 663 MET cc_start: 0.9404 (tpt) cc_final: 0.9118 (tpt) REVERT: A 675 PHE cc_start: 0.9131 (t80) cc_final: 0.8763 (t80) REVERT: A 696 MET cc_start: 0.8538 (pmm) cc_final: 0.8301 (pmm) REVERT: A 741 MET cc_start: 0.7033 (mmm) cc_final: 0.6788 (mmm) REVERT: A 795 MET cc_start: 0.8967 (mtm) cc_final: 0.8751 (mtm) REVERT: A 833 MET cc_start: 0.9118 (ptp) cc_final: 0.8854 (ptp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0883 time to fit residues: 9.1626 Evaluate side-chains 49 residues out of total 1406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 70 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 91 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.066100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.046105 restraints weight = 130589.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.046904 restraints weight = 76967.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.047401 restraints weight = 50053.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.047900 restraints weight = 36248.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.048069 restraints weight = 26444.797| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13144 Z= 0.215 Angle : 0.705 10.081 17865 Z= 0.344 Chirality : 0.042 0.207 2095 Planarity : 0.005 0.046 2240 Dihedral : 4.486 23.876 1735 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.82 (0.21), residues: 1603 helix: 1.37 (0.17), residues: 938 sheet: -0.48 (0.55), residues: 92 loop : -0.58 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 603 TYR 0.018 0.002 TYR B 278 PHE 0.023 0.002 PHE A 464 TRP 0.059 0.002 TRP B 662 HIS 0.004 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.22 (13142) covalent geometry : angle 0.70423 / 0.34 (17859) hydrogen bonds : bond 0.03928 / 2.64 ( 670) hydrogen bonds : angle 4.55550 / 3.23 ( 1950) link_NAG-ASN : bond 0.00382 / 0.18 ( 2) link_NAG-ASN : angle 1.95199 / 1.60 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2343.49 seconds wall clock time: 41 minutes 2.41 seconds (2462.41 seconds total)