Starting phenix.real_space_refine on Sat Jul 26 08:02:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e7m_27939/07_2025/8e7m_27939.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e7m_27939/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e7m_27939/07_2025/8e7m_27939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e7m_27939/07_2025/8e7m_27939.map" model { file = "/net/cci-nas-00/data/ceres_data/8e7m_27939/07_2025/8e7m_27939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e7m_27939/07_2025/8e7m_27939.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.113 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.52, per 1000 atoms: 0.91 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: 4.20 Conformation dependent library (CDL) restraints added in 978.9 milliseconds 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: 1.00 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: 3.02 Time building geometry restraints manager: 4.58 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: 14.120 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 29.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (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 TRP 0.045 0.002 TRP H 111 HIS 0.010 0.001 HIS A 265 PHE 0.014 0.001 PHE A 369 TYR 0.017 0.002 TYR H 59 ARG 0.003 0.000 ARG A 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 6) link_NAG-ASN : angle 3.33029 ( 18) link_BETA1-4 : bond 0.00274 ( 3) link_BETA1-4 : angle 1.96310 ( 9) hydrogen bonds : bond 0.17208 ( 410) hydrogen bonds : angle 6.72720 ( 1182) link_BETA1-6 : bond 0.00725 ( 2) link_BETA1-6 : angle 1.59483 ( 6) SS BOND : bond 0.00625 ( 6) SS BOND : angle 1.52266 ( 12) covalent geometry : bond 0.00375 ( 8506) covalent geometry : angle 0.75921 (11556) *********************** 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 : 0.885 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: 0.1587 time to fit residues: 23.7311 Evaluate side-chains 79 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.0570 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 578 ASN H 39 GLN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.205904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154876 restraints weight = 9437.625| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.41 r_work: 0.3480 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8523 Z= 0.136 Angle : 0.627 9.638 11601 Z= 0.313 Chirality : 0.043 0.217 1272 Planarity : 0.005 0.050 1474 Dihedral : 6.038 54.623 1328 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.56 % Allowed : 7.05 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1022 helix: 1.34 (0.26), residues: 388 sheet: 0.53 (0.34), residues: 217 loop : -0.71 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 165 HIS 0.005 0.001 HIS A 265 PHE 0.016 0.001 PHE A 369 TYR 0.013 0.001 TYR A 199 ARG 0.005 0.001 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 6) link_NAG-ASN : angle 2.94628 ( 18) link_BETA1-4 : bond 0.00246 ( 3) link_BETA1-4 : angle 1.21912 ( 9) hydrogen bonds : bond 0.05131 ( 410) hydrogen bonds : angle 5.09379 ( 1182) link_BETA1-6 : bond 0.00580 ( 2) link_BETA1-6 : angle 1.45168 ( 6) SS BOND : bond 0.00605 ( 6) SS BOND : angle 1.21667 ( 12) covalent geometry : bond 0.00295 ( 8506) covalent geometry : angle 0.61470 (11556) *********************** 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 91 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 133 CYS cc_start: 0.7962 (p) cc_final: 0.7264 (t) REVERT: A 455 MET cc_start: 0.8113 (tmm) cc_final: 0.7656 (tmm) REVERT: A 600 LYS cc_start: 0.7230 (tttt) cc_final: 0.6975 (ptmt) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.1712 time to fit residues: 23.3284 Evaluate side-chains 93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.201626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149443 restraints weight = 9582.964| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.23 r_work: 0.3382 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1642 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= 0.142 Angle : 0.590 9.945 11601 Z= 0.297 Chirality : 0.043 0.222 1272 Planarity : 0.004 0.043 1474 Dihedral : 5.675 52.701 1328 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.67 % Allowed : 9.41 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1022 helix: 1.66 (0.26), residues: 387 sheet: 1.01 (0.35), residues: 211 loop : -0.56 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 111 HIS 0.004 0.001 HIS A 265 PHE 0.017 0.002 PHE A 369 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 6) link_NAG-ASN : angle 2.51654 ( 18) link_BETA1-4 : bond 0.00303 ( 3) link_BETA1-4 : angle 1.11126 ( 9) hydrogen bonds : bond 0.05342 ( 410) hydrogen bonds : angle 4.76016 ( 1182) link_BETA1-6 : bond 0.00448 ( 2) link_BETA1-6 : angle 1.40859 ( 6) SS BOND : bond 0.00567 ( 6) SS BOND : angle 1.12557 ( 12) covalent geometry : bond 0.00325 ( 8506) covalent geometry : angle 0.58002 (11556) *********************** 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 99 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.961 Fit side-chains REVERT: A 133 CYS cc_start: 0.8082 (p) cc_final: 0.7222 (t) REVERT: A 455 MET cc_start: 0.8337 (tmm) cc_final: 0.7823 (tmm) REVERT: A 600 LYS cc_start: 0.7277 (tttt) cc_final: 0.7018 (ptmt) REVERT: H 110 ILE cc_start: 0.8077 (mt) cc_final: 0.7825 (mt) outliers start: 6 outliers final: 6 residues processed: 97 average time/residue: 0.1618 time to fit residues: 24.3514 Evaluate side-chains 94 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.0270 chunk 56 optimal weight: 0.1980 chunk 99 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.202872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151406 restraints weight = 9370.711| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.58 r_work: 0.3441 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1899 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= 0.107 Angle : 0.532 9.850 11601 Z= 0.267 Chirality : 0.040 0.221 1272 Planarity : 0.004 0.045 1474 Dihedral : 5.522 58.165 1328 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.15 % Favored : 97.75 % Rotamer: Outliers : 1.01 % Allowed : 10.53 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1022 helix: 1.84 (0.26), residues: 390 sheet: 1.29 (0.35), residues: 211 loop : -0.41 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE A 369 TYR 0.011 0.001 TYR H 80 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 6) link_NAG-ASN : angle 2.33594 ( 18) link_BETA1-4 : bond 0.00410 ( 3) link_BETA1-4 : angle 1.10360 ( 9) hydrogen bonds : bond 0.04338 ( 410) hydrogen bonds : angle 4.52295 ( 1182) link_BETA1-6 : bond 0.00393 ( 2) link_BETA1-6 : angle 1.35386 ( 6) SS BOND : bond 0.00469 ( 6) SS BOND : angle 0.92234 ( 12) covalent geometry : bond 0.00228 ( 8506) covalent geometry : angle 0.52249 (11556) *********************** 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 100 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.859 Fit side-chains REVERT: A 133 CYS cc_start: 0.8033 (p) cc_final: 0.7204 (t) REVERT: A 600 LYS cc_start: 0.7291 (tttt) cc_final: 0.7012 (ptmt) REVERT: H 110 ILE cc_start: 0.8054 (mt) cc_final: 0.7811 (mt) outliers start: 9 outliers final: 7 residues processed: 96 average time/residue: 0.1477 time to fit residues: 21.9925 Evaluate side-chains 95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 11 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.199740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146636 restraints weight = 9503.108| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.32 r_work: 0.3353 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8523 Z= 0.158 Angle : 0.639 15.119 11601 Z= 0.310 Chirality : 0.043 0.348 1272 Planarity : 0.004 0.043 1474 Dihedral : 6.033 56.577 1328 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 1.90 % Allowed : 11.42 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1022 helix: 1.81 (0.26), residues: 388 sheet: 1.39 (0.35), residues: 211 loop : -0.43 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 165 HIS 0.005 0.001 HIS L 91 PHE 0.018 0.002 PHE A 369 TYR 0.019 0.002 TYR A 385 ARG 0.005 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 6) link_NAG-ASN : angle 4.95644 ( 18) link_BETA1-4 : bond 0.00332 ( 3) link_BETA1-4 : angle 1.77951 ( 9) hydrogen bonds : bond 0.05590 ( 410) hydrogen bonds : angle 4.57442 ( 1182) link_BETA1-6 : bond 0.00567 ( 2) link_BETA1-6 : angle 1.56435 ( 6) SS BOND : bond 0.00626 ( 6) SS BOND : angle 1.24075 ( 12) covalent geometry : bond 0.00374 ( 8506) covalent geometry : angle 0.60564 (11556) *********************** 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 106 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.932 Fit side-chains REVERT: A 133 CYS cc_start: 0.8092 (p) cc_final: 0.7287 (t) REVERT: A 408 MET cc_start: 0.8060 (mmt) cc_final: 0.7845 (mmt) REVERT: A 600 LYS cc_start: 0.7331 (tttt) cc_final: 0.7038 (ptmt) REVERT: H 110 ILE cc_start: 0.8228 (mt) cc_final: 0.7956 (mt) REVERT: L 61 ARG cc_start: 0.4704 (OUTLIER) cc_final: 0.4059 (ptt180) outliers start: 17 outliers final: 12 residues processed: 98 average time/residue: 0.1535 time to fit residues: 23.2512 Evaluate side-chains 97 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 107 VAL 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 54 LEU Chi-restraints excluded: chain L residue 61 ARG 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 62 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.199397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145572 restraints weight = 9486.206| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.20 r_work: 0.3365 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8523 Z= 0.130 Angle : 0.588 13.056 11601 Z= 0.285 Chirality : 0.041 0.235 1272 Planarity : 0.004 0.044 1474 Dihedral : 5.746 58.860 1328 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Rotamer: Outliers : 1.90 % Allowed : 12.21 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1022 helix: 1.91 (0.26), residues: 388 sheet: 1.42 (0.35), residues: 206 loop : -0.43 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.015 0.001 PHE A 369 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 6) link_NAG-ASN : angle 4.17466 ( 18) link_BETA1-4 : bond 0.00295 ( 3) link_BETA1-4 : angle 1.71609 ( 9) hydrogen bonds : bond 0.04961 ( 410) hydrogen bonds : angle 4.47105 ( 1182) link_BETA1-6 : bond 0.00336 ( 2) link_BETA1-6 : angle 1.48730 ( 6) SS BOND : bond 0.00531 ( 6) SS BOND : angle 0.96567 ( 12) covalent geometry : bond 0.00296 ( 8506) covalent geometry : angle 0.56130 (11556) *********************** 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 100 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.863 Fit side-chains REVERT: A 133 CYS cc_start: 0.8096 (p) cc_final: 0.7297 (t) REVERT: A 408 MET cc_start: 0.8007 (mmt) cc_final: 0.7760 (mmt) REVERT: H 110 ILE cc_start: 0.8210 (mt) cc_final: 0.7979 (mt) REVERT: L 4 MET cc_start: 0.8172 (mmt) cc_final: 0.7620 (mmt) REVERT: L 61 ARG cc_start: 0.4570 (OUTLIER) cc_final: 0.4050 (ptt180) outliers start: 17 outliers final: 11 residues processed: 94 average time/residue: 0.1718 time to fit residues: 24.1304 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 : 0.989 ------------------------------------------------------------------------------- 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 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 61 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.0570 chunk 80 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.200719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150237 restraints weight = 9530.859| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.63 r_work: 0.3391 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8523 Z= 0.115 Angle : 0.563 11.075 11601 Z= 0.274 Chirality : 0.040 0.248 1272 Planarity : 0.004 0.043 1474 Dihedral : 5.186 58.589 1328 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1022 helix: 1.95 (0.26), residues: 396 sheet: 1.49 (0.36), residues: 206 loop : -0.43 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.001 PHE A 369 TYR 0.011 0.001 TYR H 80 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 6) link_NAG-ASN : angle 4.13607 ( 18) link_BETA1-4 : bond 0.00403 ( 3) link_BETA1-4 : angle 1.33187 ( 9) hydrogen bonds : bond 0.04559 ( 410) hydrogen bonds : angle 4.33850 ( 1182) link_BETA1-6 : bond 0.00297 ( 2) link_BETA1-6 : angle 1.61970 ( 6) SS BOND : bond 0.00492 ( 6) SS BOND : angle 0.90990 ( 12) covalent geometry : bond 0.00255 ( 8506) covalent geometry : angle 0.53691 (11556) *********************** 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 100 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.841 Fit side-chains REVERT: A 133 CYS cc_start: 0.8101 (p) cc_final: 0.7340 (t) REVERT: A 408 MET cc_start: 0.7998 (mmt) cc_final: 0.7729 (mmt) REVERT: H 110 ILE cc_start: 0.8185 (mt) cc_final: 0.7950 (mt) REVERT: L 4 MET cc_start: 0.8124 (mmt) cc_final: 0.7774 (mmt) REVERT: L 79 GLN cc_start: 0.7291 (mm-40) cc_final: 0.6356 (mp10) outliers start: 15 outliers final: 12 residues processed: 95 average time/residue: 0.1645 time to fit residues: 23.9441 Evaluate side-chains 93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.0030 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.200842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150222 restraints weight = 9540.455| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.83 r_work: 0.3385 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8523 Z= 0.115 Angle : 0.556 10.811 11601 Z= 0.272 Chirality : 0.040 0.250 1272 Planarity : 0.004 0.042 1474 Dihedral : 5.026 57.984 1328 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Rotamer: Outliers : 1.23 % Allowed : 13.66 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1022 helix: 2.10 (0.26), residues: 390 sheet: 1.56 (0.36), residues: 206 loop : -0.34 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE A 369 TYR 0.011 0.001 TYR H 80 ARG 0.006 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 6) link_NAG-ASN : angle 4.04449 ( 18) link_BETA1-4 : bond 0.00396 ( 3) link_BETA1-4 : angle 1.18385 ( 9) hydrogen bonds : bond 0.04518 ( 410) hydrogen bonds : angle 4.29481 ( 1182) link_BETA1-6 : bond 0.00190 ( 2) link_BETA1-6 : angle 1.78815 ( 6) SS BOND : bond 0.00487 ( 6) SS BOND : angle 0.92244 ( 12) covalent geometry : bond 0.00255 ( 8506) covalent geometry : angle 0.53003 (11556) *********************** 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 92 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.858 Fit side-chains REVERT: A 133 CYS cc_start: 0.8162 (p) cc_final: 0.7403 (t) REVERT: A 376 MET cc_start: 0.7866 (mmm) cc_final: 0.7577 (mmm) REVERT: A 408 MET cc_start: 0.7998 (mmt) cc_final: 0.7716 (mmt) REVERT: L 79 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6339 (mp10) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.1544 time to fit residues: 20.9789 Evaluate side-chains 89 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 91 optimal weight: 8.9990 chunk 32 optimal weight: 0.0470 chunk 67 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.200687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146721 restraints weight = 9606.528| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.45 r_work: 0.3379 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8523 Z= 0.119 Angle : 0.561 10.645 11601 Z= 0.275 Chirality : 0.040 0.253 1272 Planarity : 0.004 0.042 1474 Dihedral : 4.990 58.366 1328 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.46 % Allowed : 13.66 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1022 helix: 2.10 (0.26), residues: 390 sheet: 1.59 (0.36), residues: 206 loop : -0.32 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.001 PHE A 369 TYR 0.011 0.001 TYR A 385 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 6) link_NAG-ASN : angle 3.96904 ( 18) link_BETA1-4 : bond 0.00375 ( 3) link_BETA1-4 : angle 1.12359 ( 9) hydrogen bonds : bond 0.04581 ( 410) hydrogen bonds : angle 4.28731 ( 1182) link_BETA1-6 : bond 0.00152 ( 2) link_BETA1-6 : angle 1.78423 ( 6) SS BOND : bond 0.00494 ( 6) SS BOND : angle 0.94940 ( 12) covalent geometry : bond 0.00270 ( 8506) covalent geometry : angle 0.53686 (11556) *********************** 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 96 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.858 Fit side-chains REVERT: A 133 CYS cc_start: 0.8142 (p) cc_final: 0.7404 (t) REVERT: A 408 MET cc_start: 0.7997 (mmt) cc_final: 0.7728 (mmt) REVERT: L 79 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6486 (mp10) outliers start: 13 outliers final: 12 residues processed: 92 average time/residue: 0.1596 time to fit residues: 22.7738 Evaluate side-chains 91 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 90 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4244 r_free = 0.4244 target = 0.199752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148677 restraints weight = 9534.892| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.02 r_work: 0.3368 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8523 Z= 0.128 Angle : 0.570 10.681 11601 Z= 0.280 Chirality : 0.041 0.253 1272 Planarity : 0.004 0.041 1474 Dihedral : 5.007 58.404 1328 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.46 % Allowed : 14.00 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.27), residues: 1022 helix: 2.06 (0.26), residues: 390 sheet: 1.59 (0.36), residues: 206 loop : -0.31 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.004 0.001 HIS L 91 PHE 0.015 0.001 PHE A 369 TYR 0.021 0.001 TYR H 80 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 6) link_NAG-ASN : angle 3.94267 ( 18) link_BETA1-4 : bond 0.00376 ( 3) link_BETA1-4 : angle 1.08196 ( 9) hydrogen bonds : bond 0.04799 ( 410) hydrogen bonds : angle 4.29582 ( 1182) link_BETA1-6 : bond 0.00256 ( 2) link_BETA1-6 : angle 1.79991 ( 6) SS BOND : bond 0.00493 ( 6) SS BOND : angle 1.01240 ( 12) covalent geometry : bond 0.00294 ( 8506) covalent geometry : angle 0.54658 (11556) ********************** 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 95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.836 Fit side-chains REVERT: A 133 CYS cc_start: 0.8143 (p) cc_final: 0.7419 (t) REVERT: A 408 MET cc_start: 0.8015 (mmt) cc_final: 0.7765 (mmt) REVERT: L 78 LEU cc_start: 0.5460 (mt) cc_final: 0.5239 (mp) REVERT: L 93 TYR cc_start: 0.7859 (t80) cc_final: 0.7563 (m-80) outliers start: 13 outliers final: 12 residues processed: 91 average time/residue: 0.1521 time to fit residues: 21.5273 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 : 0.931 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 0.0370 chunk 98 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 30.0000 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.199266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146838 restraints weight = 9611.913| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.15 r_work: 0.3366 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8523 Z= 0.130 Angle : 0.572 10.648 11601 Z= 0.282 Chirality : 0.041 0.254 1272 Planarity : 0.004 0.041 1474 Dihedral : 5.013 58.491 1328 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 1022 helix: 1.97 (0.26), residues: 396 sheet: 1.59 (0.37), residues: 206 loop : -0.34 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.001 PHE A 369 TYR 0.013 0.001 TYR A 385 ARG 0.005 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 6) link_NAG-ASN : angle 3.91665 ( 18) link_BETA1-4 : bond 0.00341 ( 3) link_BETA1-4 : angle 1.05618 ( 9) hydrogen bonds : bond 0.04866 ( 410) hydrogen bonds : angle 4.31480 ( 1182) link_BETA1-6 : bond 0.00198 ( 2) link_BETA1-6 : angle 1.77687 ( 6) SS BOND : bond 0.00511 ( 6) SS BOND : angle 1.04491 ( 12) covalent geometry : bond 0.00299 ( 8506) covalent geometry : angle 0.54881 (11556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6645.87 seconds wall clock time: 118 minutes 53.21 seconds (7133.21 seconds total)