Starting phenix.real_space_refine on Fri Aug 22 23:01:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e7m_27939/08_2025/8e7m_27939.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e7m_27939/08_2025/8e7m_27939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e7m_27939/08_2025/8e7m_27939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e7m_27939/08_2025/8e7m_27939.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e7m_27939/08_2025/8e7m_27939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e7m_27939/08_2025/8e7m_27939.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.113 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 44 5.16 5 C 5261 2.51 5 N 1365 2.21 5 O 1623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8293 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4876 Classifications: {'peptide': 598} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 570} Chain: "H" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1616 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Chain: "L" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1655 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.96, per 1000 atoms: 0.24 Number of scatterers: 8293 At special positions: 0 Unit cell: (72.828, 76.296, 162.129, 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 44 16.00 O 1623 8.00 N 1365 7.00 C 5261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG C 1 " - " FUC C 3 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 322 " " NAG A 703 " - " ASN A 432 " " NAG B 1 " - " ASN A 90 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 449.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 13 sheets defined 44.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 19 through 52 removed outlier: 3.925A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.611A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 4.638A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 4.013A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.656A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 414 removed outlier: 3.577A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.019A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.613A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 486 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.845A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.850A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.691A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.543A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 166 No H-bonds generated for 'chain 'H' and resid 164 through 166' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.527A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.276A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.161A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.554A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.122A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 188 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 128 through 132 removed outlier: 4.122A pdb=" N GLY H 147 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 188 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 159 through 162 removed outlier: 4.601A pdb=" N TYR H 202 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 219 " --> pdb=" O TYR H 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.840A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.640A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.640A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.637A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.778A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1182 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: 1.40 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: 2633 1.34 - 1.46: 2140 1.46 - 1.59: 3662 1.59 - 1.71: 0 1.71 - 1.83: 71 Bond restraints: 8506 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.34e+00 bond pdb=" C2 NAG C 1 " pdb=" N2 NAG C 1 " ideal model delta sigma weight residual 1.439 1.465 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 8501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 11131 1.76 - 3.52: 347 3.52 - 5.29: 59 5.29 - 7.05: 11 7.05 - 8.81: 8 Bond angle restraints: 11556 Sorted by residual: angle pdb=" CA GLN A 18 " pdb=" CB GLN A 18 " pdb=" CG GLN A 18 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" C ALA A 17 " pdb=" N GLN A 18 " pdb=" CA GLN A 18 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N GLN A 18 " pdb=" CA GLN A 18 " pdb=" CB GLN A 18 " ideal model delta sigma weight residual 110.49 115.51 -5.02 1.69e+00 3.50e-01 8.83e+00 angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 104.05 8.65 3.00e+00 1.11e-01 8.31e+00 angle pdb=" N ARG A 177 " pdb=" CA ARG A 177 " pdb=" C ARG A 177 " ideal model delta sigma weight residual 109.81 116.13 -6.32 2.21e+00 2.05e-01 8.19e+00 ... (remaining 11551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4648 16.25 - 32.50: 403 32.50 - 48.75: 98 48.75 - 65.00: 21 65.00 - 81.25: 12 Dihedral angle restraints: 5182 sinusoidal: 2184 harmonic: 2998 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 35.54 57.46 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CA SER H 123 " pdb=" C SER H 123 " pdb=" N THR H 124 " pdb=" CA THR H 124 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASN A 322 " pdb=" C ASN A 322 " pdb=" N MET A 323 " pdb=" CA MET A 323 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 915 0.047 - 0.095: 267 0.095 - 0.142: 79 0.142 - 0.189: 9 0.189 - 0.236: 2 Chirality restraints: 1272 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA MET A 82 " pdb=" N MET A 82 " pdb=" C MET A 82 " pdb=" CB MET A 82 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 1269 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 335 " 0.052 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 336 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 111 " 0.017 2.00e-02 2.50e+03 1.73e-02 7.52e+00 pdb=" CG TRP H 111 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP H 111 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 111 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 111 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 111 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 111 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 415 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.029 5.00e-02 4.00e+02 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 183 2.70 - 3.25: 8023 3.25 - 3.80: 12517 3.80 - 4.35: 16053 4.35 - 4.90: 27258 Nonbonded interactions: 64034 Sorted by model distance: nonbonded pdb=" OD1 ASP A 269 " pdb=" N MET A 270 " model vdw 2.154 3.120 nonbonded pdb=" OG SER A 420 " pdb=" O7 NAG D 1 " model vdw 2.180 3.040 nonbonded pdb=" O GLN L 124 " pdb=" OG SER L 127 " model vdw 2.267 3.040 nonbonded pdb=" OE1 GLU A 23 " pdb=" OH TYR H 59 " model vdw 2.299 3.040 nonbonded pdb=" OD1 ASN A 90 " pdb=" N2 NAG B 1 " model vdw 2.304 3.120 ... (remaining 64029 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.570 Find NCS groups from input model: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8523 Z= 0.175 Angle : 0.773 8.809 11601 Z= 0.390 Chirality : 0.049 0.236 1272 Planarity : 0.005 0.081 1474 Dihedral : 13.529 81.248 3240 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: -1.04 (0.23), residues: 1022 helix: -0.16 (0.23), residues: 390 sheet: -0.25 (0.33), residues: 210 loop : -1.32 (0.26), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 204 TYR 0.017 0.002 TYR H 59 PHE 0.014 0.001 PHE A 369 TRP 0.045 0.002 TRP H 111 HIS 0.010 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8506) covalent geometry : angle 0.75921 (11556) SS BOND : bond 0.00625 ( 6) SS BOND : angle 1.52266 ( 12) hydrogen bonds : bond 0.17208 ( 410) hydrogen bonds : angle 6.72720 ( 1182) link_BETA1-4 : bond 0.00274 ( 3) link_BETA1-4 : angle 1.96310 ( 9) link_BETA1-6 : bond 0.00725 ( 2) link_BETA1-6 : angle 1.59483 ( 6) link_NAG-ASN : bond 0.00721 ( 6) link_NAG-ASN : angle 3.33029 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 133 CYS cc_start: 0.7556 (p) cc_final: 0.7201 (t) REVERT: A 206 ASP cc_start: 0.7581 (t0) cc_final: 0.7217 (t0) REVERT: L 4 MET cc_start: 0.7777 (mmt) cc_final: 0.7223 (mmt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0710 time to fit residues: 10.8594 Evaluate side-chains 78 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 50.0000 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 572 ASN A 578 ASN H 39 GLN H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.205612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153873 restraints weight = 9491.543| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.50 r_work: 0.3472 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8523 Z= 0.137 Angle : 0.629 9.785 11601 Z= 0.314 Chirality : 0.043 0.215 1272 Planarity : 0.005 0.050 1474 Dihedral : 6.031 54.582 1328 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.67 % Allowed : 6.83 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 0.50 (0.25), residues: 1022 helix: 1.35 (0.26), residues: 388 sheet: 0.52 (0.34), residues: 217 loop : -0.70 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 169 TYR 0.014 0.001 TYR A 199 PHE 0.016 0.001 PHE A 369 TRP 0.018 0.001 TRP A 165 HIS 0.006 0.001 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8506) covalent geometry : angle 0.61583 (11556) SS BOND : bond 0.00614 ( 6) SS BOND : angle 1.26552 ( 12) hydrogen bonds : bond 0.05139 ( 410) hydrogen bonds : angle 5.07135 ( 1182) link_BETA1-4 : bond 0.00258 ( 3) link_BETA1-4 : angle 1.20131 ( 9) link_BETA1-6 : bond 0.00579 ( 2) link_BETA1-6 : angle 1.44637 ( 6) link_NAG-ASN : bond 0.00568 ( 6) link_NAG-ASN : angle 2.94556 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 133 CYS cc_start: 0.7976 (p) cc_final: 0.7260 (t) REVERT: A 455 MET cc_start: 0.8129 (tmm) cc_final: 0.7663 (tmm) REVERT: A 600 LYS cc_start: 0.7235 (tttt) cc_final: 0.6978 (ptmt) REVERT: H 110 ILE cc_start: 0.7976 (mp) cc_final: 0.7531 (mt) outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.0678 time to fit residues: 9.0407 Evaluate side-chains 93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 99 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN L 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.196771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144292 restraints weight = 9475.388| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.99 r_work: 0.3340 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8523 Z= 0.183 Angle : 0.647 10.102 11601 Z= 0.329 Chirality : 0.045 0.256 1272 Planarity : 0.005 0.042 1474 Dihedral : 5.853 50.636 1328 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.01 % Allowed : 9.85 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 0.73 (0.26), residues: 1022 helix: 1.42 (0.26), residues: 387 sheet: 1.05 (0.35), residues: 210 loop : -0.66 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 72 TYR 0.024 0.002 TYR A 385 PHE 0.021 0.002 PHE A 369 TRP 0.021 0.002 TRP H 111 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8506) covalent geometry : angle 0.63774 (11556) SS BOND : bond 0.00666 ( 6) SS BOND : angle 1.31303 ( 12) hydrogen bonds : bond 0.06456 ( 410) hydrogen bonds : angle 4.86830 ( 1182) link_BETA1-4 : bond 0.00227 ( 3) link_BETA1-4 : angle 1.20089 ( 9) link_BETA1-6 : bond 0.00493 ( 2) link_BETA1-6 : angle 1.50238 ( 6) link_NAG-ASN : bond 0.00378 ( 6) link_NAG-ASN : angle 2.48379 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.203 Fit side-chains REVERT: A 133 CYS cc_start: 0.8057 (p) cc_final: 0.7241 (t) REVERT: A 600 LYS cc_start: 0.7333 (tttt) cc_final: 0.7061 (ptmt) REVERT: H 110 ILE cc_start: 0.8110 (mp) cc_final: 0.7830 (mt) outliers start: 9 outliers final: 7 residues processed: 98 average time/residue: 0.0552 time to fit residues: 8.3599 Evaluate side-chains 93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.0050 chunk 79 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.197307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144405 restraints weight = 9580.236| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.19 r_work: 0.3335 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8523 Z= 0.159 Angle : 0.594 9.852 11601 Z= 0.301 Chirality : 0.043 0.241 1272 Planarity : 0.004 0.045 1474 Dihedral : 5.810 58.254 1328 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 1.57 % Allowed : 12.32 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 0.86 (0.26), residues: 1022 helix: 1.50 (0.26), residues: 387 sheet: 1.24 (0.35), residues: 207 loop : -0.61 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 61 TYR 0.016 0.001 TYR A 385 PHE 0.018 0.002 PHE A 369 TRP 0.021 0.001 TRP H 111 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8506) covalent geometry : angle 0.58516 (11556) SS BOND : bond 0.00614 ( 6) SS BOND : angle 1.14590 ( 12) hydrogen bonds : bond 0.05717 ( 410) hydrogen bonds : angle 4.71593 ( 1182) link_BETA1-4 : bond 0.00265 ( 3) link_BETA1-4 : angle 1.04732 ( 9) link_BETA1-6 : bond 0.00375 ( 2) link_BETA1-6 : angle 1.54679 ( 6) link_NAG-ASN : bond 0.00337 ( 6) link_NAG-ASN : angle 2.28615 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.320 Fit side-chains REVERT: A 133 CYS cc_start: 0.8097 (p) cc_final: 0.7302 (t) REVERT: A 455 MET cc_start: 0.8414 (tmm) cc_final: 0.7871 (tmm) REVERT: A 600 LYS cc_start: 0.7333 (tttt) cc_final: 0.7015 (ptmt) REVERT: H 110 ILE cc_start: 0.8087 (mp) cc_final: 0.7857 (mt) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.0585 time to fit residues: 8.7618 Evaluate side-chains 91 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 8 optimal weight: 0.9980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.200202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.146298 restraints weight = 9439.879| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.09 r_work: 0.3339 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8523 Z= 0.143 Angle : 0.573 9.865 11601 Z= 0.290 Chirality : 0.042 0.233 1272 Planarity : 0.004 0.044 1474 Dihedral : 5.640 53.427 1328 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 1.68 % Allowed : 12.99 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 0.97 (0.26), residues: 1022 helix: 1.61 (0.26), residues: 388 sheet: 1.37 (0.35), residues: 206 loop : -0.62 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.014 0.001 TYR A 385 PHE 0.017 0.001 PHE A 369 TRP 0.014 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8506) covalent geometry : angle 0.56437 (11556) SS BOND : bond 0.00580 ( 6) SS BOND : angle 1.01690 ( 12) hydrogen bonds : bond 0.05447 ( 410) hydrogen bonds : angle 4.61625 ( 1182) link_BETA1-4 : bond 0.00254 ( 3) link_BETA1-4 : angle 1.03848 ( 9) link_BETA1-6 : bond 0.00306 ( 2) link_BETA1-6 : angle 1.51418 ( 6) link_NAG-ASN : bond 0.00329 ( 6) link_NAG-ASN : angle 2.18510 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.278 Fit side-chains REVERT: A 133 CYS cc_start: 0.8117 (p) cc_final: 0.7309 (t) REVERT: H 110 ILE cc_start: 0.8207 (mp) cc_final: 0.7908 (mt) REVERT: L 4 MET cc_start: 0.8243 (mmt) cc_final: 0.7704 (mmt) REVERT: L 78 LEU cc_start: 0.5190 (mt) cc_final: 0.4851 (mt) REVERT: L 79 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6498 (mm110) outliers start: 15 outliers final: 12 residues processed: 99 average time/residue: 0.0740 time to fit residues: 11.0429 Evaluate side-chains 99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.196308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143902 restraints weight = 9455.917| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.09 r_work: 0.3305 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8523 Z= 0.182 Angle : 0.607 9.898 11601 Z= 0.309 Chirality : 0.043 0.245 1272 Planarity : 0.004 0.044 1474 Dihedral : 5.565 51.412 1328 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Rotamer: Outliers : 2.02 % Allowed : 13.33 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 0.90 (0.26), residues: 1022 helix: 1.52 (0.26), residues: 388 sheet: 1.37 (0.36), residues: 206 loop : -0.65 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.018 0.002 TYR A 385 PHE 0.018 0.002 PHE A 369 TRP 0.014 0.001 TRP A 165 HIS 0.005 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8506) covalent geometry : angle 0.59919 (11556) SS BOND : bond 0.00671 ( 6) SS BOND : angle 1.22424 ( 12) hydrogen bonds : bond 0.06213 ( 410) hydrogen bonds : angle 4.63731 ( 1182) link_BETA1-4 : bond 0.00209 ( 3) link_BETA1-4 : angle 1.02220 ( 9) link_BETA1-6 : bond 0.00387 ( 2) link_BETA1-6 : angle 1.64644 ( 6) link_NAG-ASN : bond 0.00305 ( 6) link_NAG-ASN : angle 2.05295 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.301 Fit side-chains REVERT: A 133 CYS cc_start: 0.8193 (p) cc_final: 0.7380 (t) REVERT: H 13 GLN cc_start: 0.6615 (mm110) cc_final: 0.6187 (tp-100) REVERT: H 110 ILE cc_start: 0.8229 (mt) cc_final: 0.7954 (mt) REVERT: L 78 LEU cc_start: 0.5177 (mt) cc_final: 0.4820 (mt) REVERT: L 79 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6638 (mm-40) outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 0.0641 time to fit residues: 9.8821 Evaluate side-chains 96 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 108 PHE Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.197549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144211 restraints weight = 9495.840| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.29 r_work: 0.3318 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8523 Z= 0.157 Angle : 0.576 9.817 11601 Z= 0.293 Chirality : 0.042 0.240 1272 Planarity : 0.004 0.044 1474 Dihedral : 5.366 52.860 1328 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.46 % Allowed : 14.11 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 0.97 (0.26), residues: 1022 helix: 1.61 (0.26), residues: 388 sheet: 1.40 (0.36), residues: 206 loop : -0.64 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.014 0.001 TYR A 385 PHE 0.016 0.002 PHE A 369 TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 540 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8506) covalent geometry : angle 0.56910 (11556) SS BOND : bond 0.00572 ( 6) SS BOND : angle 1.02484 ( 12) hydrogen bonds : bond 0.05579 ( 410) hydrogen bonds : angle 4.52659 ( 1182) link_BETA1-4 : bond 0.00323 ( 3) link_BETA1-4 : angle 1.00661 ( 9) link_BETA1-6 : bond 0.00327 ( 2) link_BETA1-6 : angle 1.49246 ( 6) link_NAG-ASN : bond 0.00295 ( 6) link_NAG-ASN : angle 1.97041 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.304 Fit side-chains REVERT: A 133 CYS cc_start: 0.8197 (p) cc_final: 0.7436 (t) REVERT: H 13 GLN cc_start: 0.6775 (mm110) cc_final: 0.6293 (tp-100) REVERT: H 110 ILE cc_start: 0.8223 (mt) cc_final: 0.7940 (mt) REVERT: L 78 LEU cc_start: 0.5175 (mt) cc_final: 0.4863 (mt) REVERT: L 79 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6704 (mm110) outliers start: 13 outliers final: 12 residues processed: 91 average time/residue: 0.0650 time to fit residues: 9.3238 Evaluate side-chains 92 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 97 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.198267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144780 restraints weight = 9306.531| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 3.01 r_work: 0.3311 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8523 Z= 0.109 Angle : 0.527 9.761 11601 Z= 0.266 Chirality : 0.040 0.223 1272 Planarity : 0.004 0.043 1474 Dihedral : 4.970 54.322 1328 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.46 % Allowed : 14.67 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 1.22 (0.27), residues: 1022 helix: 1.85 (0.27), residues: 390 sheet: 1.47 (0.37), residues: 206 loop : -0.51 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.011 0.001 TYR A 516 PHE 0.016 0.001 PHE A 327 TRP 0.013 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8506) covalent geometry : angle 0.52050 (11556) SS BOND : bond 0.00441 ( 6) SS BOND : angle 0.79054 ( 12) hydrogen bonds : bond 0.04458 ( 410) hydrogen bonds : angle 4.37139 ( 1182) link_BETA1-4 : bond 0.00371 ( 3) link_BETA1-4 : angle 1.07191 ( 9) link_BETA1-6 : bond 0.00372 ( 2) link_BETA1-6 : angle 1.32604 ( 6) link_NAG-ASN : bond 0.00372 ( 6) link_NAG-ASN : angle 1.92025 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.211 Fit side-chains REVERT: A 133 CYS cc_start: 0.8125 (p) cc_final: 0.7310 (t) REVERT: A 323 MET cc_start: 0.8142 (mmt) cc_final: 0.7872 (mmt) REVERT: H 13 GLN cc_start: 0.6786 (mm110) cc_final: 0.6254 (tp40) REVERT: H 99 ASP cc_start: 0.8597 (t0) cc_final: 0.8381 (m-30) REVERT: L 78 LEU cc_start: 0.5224 (mt) cc_final: 0.4952 (mt) REVERT: L 79 GLN cc_start: 0.6843 (mm-40) cc_final: 0.6466 (mm-40) REVERT: L 100 GLN cc_start: 0.8774 (mp10) cc_final: 0.8462 (mp10) outliers start: 13 outliers final: 12 residues processed: 96 average time/residue: 0.0671 time to fit residues: 10.0353 Evaluate side-chains 94 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.196032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.141462 restraints weight = 9274.710| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.15 r_work: 0.3248 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8523 Z= 0.149 Angle : 0.563 9.843 11601 Z= 0.285 Chirality : 0.042 0.228 1272 Planarity : 0.004 0.043 1474 Dihedral : 5.042 52.953 1328 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.46 % Allowed : 14.78 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 1.16 (0.26), residues: 1022 helix: 1.81 (0.26), residues: 388 sheet: 1.50 (0.37), residues: 206 loop : -0.57 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.013 0.001 TYR A 385 PHE 0.015 0.001 PHE A 369 TRP 0.014 0.001 TRP A 165 HIS 0.004 0.001 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8506) covalent geometry : angle 0.55628 (11556) SS BOND : bond 0.00581 ( 6) SS BOND : angle 1.03769 ( 12) hydrogen bonds : bond 0.05254 ( 410) hydrogen bonds : angle 4.39800 ( 1182) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 1.04139 ( 9) link_BETA1-6 : bond 0.00319 ( 2) link_BETA1-6 : angle 1.47715 ( 6) link_NAG-ASN : bond 0.00290 ( 6) link_NAG-ASN : angle 1.89383 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.193 Fit side-chains REVERT: A 133 CYS cc_start: 0.8133 (p) cc_final: 0.7350 (t) REVERT: A 394 ASN cc_start: 0.8314 (t0) cc_final: 0.8054 (m-40) REVERT: L 78 LEU cc_start: 0.5188 (mt) cc_final: 0.4903 (mt) REVERT: L 79 GLN cc_start: 0.6803 (mm-40) cc_final: 0.6407 (mm-40) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.0506 time to fit residues: 7.3874 Evaluate side-chains 91 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 63 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 96 optimal weight: 0.0070 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.198680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147054 restraints weight = 9196.042| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.89 r_work: 0.3346 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8523 Z= 0.105 Angle : 0.527 9.763 11601 Z= 0.264 Chirality : 0.040 0.216 1272 Planarity : 0.004 0.042 1474 Dihedral : 4.823 54.790 1328 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.12 % Allowed : 14.67 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 1.34 (0.27), residues: 1022 helix: 1.96 (0.27), residues: 390 sheet: 1.56 (0.37), residues: 206 loop : -0.46 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.012 0.001 TYR A 516 PHE 0.016 0.001 PHE A 327 TRP 0.013 0.001 TRP A 165 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8506) covalent geometry : angle 0.52042 (11556) SS BOND : bond 0.00425 ( 6) SS BOND : angle 0.72179 ( 12) hydrogen bonds : bond 0.04159 ( 410) hydrogen bonds : angle 4.27906 ( 1182) link_BETA1-4 : bond 0.00356 ( 3) link_BETA1-4 : angle 1.04926 ( 9) link_BETA1-6 : bond 0.00345 ( 2) link_BETA1-6 : angle 1.29407 ( 6) link_NAG-ASN : bond 0.00358 ( 6) link_NAG-ASN : angle 1.86651 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.331 Fit side-chains REVERT: A 133 CYS cc_start: 0.7969 (p) cc_final: 0.7216 (t) REVERT: A 376 MET cc_start: 0.7704 (mmm) cc_final: 0.7495 (tpp) REVERT: A 394 ASN cc_start: 0.8245 (t0) cc_final: 0.7991 (m-40) REVERT: H 13 GLN cc_start: 0.6766 (mm110) cc_final: 0.6240 (tp40) REVERT: L 78 LEU cc_start: 0.5182 (mt) cc_final: 0.4909 (mt) REVERT: L 79 GLN cc_start: 0.6679 (mm-40) cc_final: 0.6387 (mm110) REVERT: L 100 GLN cc_start: 0.8787 (mp10) cc_final: 0.8438 (mp10) outliers start: 10 outliers final: 8 residues processed: 94 average time/residue: 0.0684 time to fit residues: 10.0398 Evaluate side-chains 92 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 63 optimal weight: 0.0010 chunk 57 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.198328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146137 restraints weight = 9216.852| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.95 r_work: 0.3322 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8523 Z= 0.122 Angle : 0.549 9.798 11601 Z= 0.276 Chirality : 0.041 0.217 1272 Planarity : 0.004 0.041 1474 Dihedral : 4.825 53.650 1328 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.78 % Allowed : 15.34 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 aren not related in a simple way. whole: 1.38 (0.27), residues: 1022 helix: 1.98 (0.27), residues: 390 sheet: 1.58 (0.37), residues: 206 loop : -0.44 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.020 0.001 TYR H 80 PHE 0.014 0.001 PHE A 327 TRP 0.014 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8506) covalent geometry : angle 0.54215 (11556) SS BOND : bond 0.00496 ( 6) SS BOND : angle 0.99738 ( 12) hydrogen bonds : bond 0.04652 ( 410) hydrogen bonds : angle 4.28122 ( 1182) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.02187 ( 9) link_BETA1-6 : bond 0.00354 ( 2) link_BETA1-6 : angle 1.41593 ( 6) link_NAG-ASN : bond 0.00303 ( 6) link_NAG-ASN : angle 1.83651 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.42 seconds wall clock time: 32 minutes 22.16 seconds (1942.16 seconds total)