Starting phenix.real_space_refine on Thu Mar 13 00:39:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e7m_27939/03_2025/8e7m_27939.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e7m_27939/03_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_27939/03_2025/8e7m_27939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e7m_27939/03_2025/8e7m_27939.map" model { file = "/net/cci-nas-00/data/ceres_data/8e7m_27939/03_2025/8e7m_27939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e7m_27939/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.92, per 1000 atoms: 0.71 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: 2.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.93 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: 2.38 Time building geometry restraints manager: 2.53 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- 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 8506 Z= 0.247 Angle : 0.759 8.809 11556 Z= 0.387 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 *********************** 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 : 0.855 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: 0.1694 time to fit residues: 25.2527 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 : 0.832 ------------------------------------------------------------------------------- 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: 0.7980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.205729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154274 restraints weight = 9436.071| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.41 r_work: 0.3476 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8506 Z= 0.194 Angle : 0.615 9.681 11556 Z= 0.312 Chirality : 0.043 0.221 1272 Planarity : 0.005 0.050 1474 Dihedral : 6.047 54.575 1328 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.56 % Allowed : 6.94 % 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 (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: 0.48 (0.25), residues: 1022 helix: 1.33 (0.26), residues: 388 sheet: 0.55 (0.34), residues: 217 loop : -0.73 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 165 HIS 0.006 0.001 HIS A 265 PHE 0.016 0.001 PHE A 369 TYR 0.013 0.001 TYR A 385 ARG 0.005 0.001 ARG A 169 *********************** 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 : 0.772 Fit side-chains revert: symmetry clash REVERT: A 133 CYS cc_start: 0.7966 (p) cc_final: 0.7242 (t) REVERT: A 600 LYS cc_start: 0.7207 (tttt) cc_final: 0.6953 (ptmt) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.1573 time to fit residues: 21.4727 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 : 0.822 ------------------------------------------------------------------------------- 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: 7.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 30 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.202304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151666 restraints weight = 9449.751| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.79 r_work: 0.3413 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8506 Z= 0.185 Angle : 0.563 9.958 11556 Z= 0.285 Chirality : 0.042 0.220 1272 Planarity : 0.004 0.043 1474 Dihedral : 5.624 53.413 1328 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.67 % Allowed : 9.18 % Favored : 90.15 % 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: 0.98 (0.26), residues: 1022 helix: 1.72 (0.26), residues: 387 sheet: 1.04 (0.35), residues: 211 loop : -0.54 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 165 HIS 0.004 0.001 HIS A 265 PHE 0.015 0.001 PHE A 369 TYR 0.013 0.001 TYR A 385 ARG 0.003 0.000 ARG A 169 *********************** 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 97 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.934 Fit side-chains REVERT: A 133 CYS cc_start: 0.8059 (p) cc_final: 0.7222 (t) REVERT: A 455 MET cc_start: 0.8274 (tmm) cc_final: 0.7768 (tmm) REVERT: A 600 LYS cc_start: 0.7254 (tttt) cc_final: 0.6995 (ptmt) REVERT: H 110 ILE cc_start: 0.8027 (mt) cc_final: 0.7781 (mt) outliers start: 6 outliers final: 6 residues processed: 95 average time/residue: 0.1589 time to fit residues: 23.2140 Evaluate side-chains 95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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: 20.0000 chunk 56 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.199712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147684 restraints weight = 9501.658| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.09 r_work: 0.3370 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8506 Z= 0.212 Angle : 0.566 9.890 11556 Z= 0.289 Chirality : 0.042 0.226 1272 Planarity : 0.004 0.044 1474 Dihedral : 5.627 57.919 1328 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 1.23 % Allowed : 10.64 % Favored : 88.13 % 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: 1.09 (0.26), residues: 1022 helix: 1.73 (0.26), residues: 387 sheet: 1.31 (0.35), residues: 210 loop : -0.51 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 111 HIS 0.005 0.001 HIS L 91 PHE 0.016 0.002 PHE A 369 TYR 0.017 0.002 TYR A 385 ARG 0.002 0.000 ARG L 46 *********************** 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: 11 poor density : 89 time to evaluate : 0.863 Fit side-chains REVERT: A 133 CYS cc_start: 0.8043 (p) cc_final: 0.7209 (t) REVERT: A 586 ASN cc_start: 0.8066 (t0) cc_final: 0.7839 (t0) REVERT: A 600 LYS cc_start: 0.7310 (tttt) cc_final: 0.7022 (ptmt) REVERT: H 110 ILE cc_start: 0.8148 (mt) cc_final: 0.7858 (mt) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.1484 time to fit residues: 22.2604 Evaluate side-chains 96 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 9 optimal weight: 0.0060 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 97 optimal weight: 9.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.201675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148823 restraints weight = 9225.114| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.79 r_work: 0.3364 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8506 Z= 0.142 Angle : 0.513 9.783 11556 Z= 0.260 Chirality : 0.040 0.219 1272 Planarity : 0.004 0.045 1474 Dihedral : 5.245 54.748 1328 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.15 % Favored : 97.75 % Rotamer: Outliers : 1.01 % Allowed : 12.21 % Favored : 86.79 % 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: 1.38 (0.26), residues: 1022 helix: 1.96 (0.27), residues: 391 sheet: 1.42 (0.36), residues: 211 loop : -0.34 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 A 516 ARG 0.004 0.000 ARG L 61 *********************** 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 96 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.338 Fit side-chains REVERT: A 133 CYS cc_start: 0.8037 (p) cc_final: 0.7107 (t) REVERT: A 600 LYS cc_start: 0.7058 (tttt) cc_final: 0.6809 (ptmt) REVERT: H 110 ILE cc_start: 0.8127 (mt) cc_final: 0.7914 (mt) REVERT: L 4 MET cc_start: 0.7808 (mmt) cc_final: 0.7539 (mmt) outliers start: 9 outliers final: 8 residues processed: 91 average time/residue: 0.1817 time to fit residues: 25.9596 Evaluate side-chains 91 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.199177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.147089 restraints weight = 9534.806| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.08 r_work: 0.3366 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8506 Z= 0.217 Angle : 0.545 9.835 11556 Z= 0.279 Chirality : 0.042 0.219 1272 Planarity : 0.004 0.043 1474 Dihedral : 5.179 52.572 1328 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 1.68 % Allowed : 12.21 % 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 (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: 1.32 (0.26), residues: 1022 helix: 1.93 (0.26), residues: 388 sheet: 1.50 (0.36), residues: 206 loop : -0.41 (0.29), residues: 428 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 0.016 0.001 PHE A 369 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG L 61 *********************** 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 98 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.913 Fit side-chains REVERT: A 133 CYS cc_start: 0.8115 (p) cc_final: 0.7330 (t) REVERT: A 408 MET cc_start: 0.8059 (mmt) cc_final: 0.7779 (mmt) REVERT: A 455 MET cc_start: 0.8443 (tmm) cc_final: 0.7871 (tmm) REVERT: A 600 LYS cc_start: 0.7289 (tttt) cc_final: 0.7002 (ptmt) REVERT: H 110 ILE cc_start: 0.8184 (mt) cc_final: 0.7937 (mt) outliers start: 15 outliers final: 12 residues processed: 93 average time/residue: 0.1777 time to fit residues: 24.8570 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 : 0.848 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.196354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.143045 restraints weight = 9261.739| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.90 r_work: 0.3297 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8506 Z= 0.214 Angle : 0.552 9.782 11556 Z= 0.282 Chirality : 0.042 0.224 1272 Planarity : 0.004 0.043 1474 Dihedral : 5.137 52.958 1328 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.68 % Allowed : 12.77 % Favored : 85.55 % 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: 1.28 (0.26), residues: 1022 helix: 1.91 (0.26), residues: 388 sheet: 1.52 (0.36), residues: 206 loop : -0.49 (0.29), residues: 428 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 0.016 0.001 PHE A 369 TYR 0.016 0.001 TYR A 385 ARG 0.008 0.000 ARG L 61 *********************** 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 101 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.938 Fit side-chains REVERT: A 133 CYS cc_start: 0.8145 (p) cc_final: 0.7270 (t) REVERT: A 408 MET cc_start: 0.7783 (mmt) cc_final: 0.7513 (mmt) REVERT: H 110 ILE cc_start: 0.8227 (mt) cc_final: 0.7988 (mt) outliers start: 15 outliers final: 13 residues processed: 98 average time/residue: 0.1798 time to fit residues: 26.8447 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 : 0.837 ------------------------------------------------------------------------------- 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 398 GLU 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: 10.0000 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.196138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143455 restraints weight = 9308.803| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.81 r_work: 0.3311 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8506 Z= 0.203 Angle : 0.548 9.800 11556 Z= 0.280 Chirality : 0.041 0.222 1272 Planarity : 0.004 0.042 1474 Dihedral : 5.084 53.039 1328 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: 1.33 (0.26), residues: 1022 helix: 1.96 (0.26), residues: 388 sheet: 1.53 (0.36), residues: 206 loop : -0.47 (0.29), residues: 428 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 0.017 0.001 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.007 0.000 ARG L 61 *********************** 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 : 0.870 Fit side-chains REVERT: A 133 CYS cc_start: 0.8113 (p) cc_final: 0.7250 (t) REVERT: A 408 MET cc_start: 0.7664 (mmt) cc_final: 0.7405 (mmt) REVERT: H 91 THR cc_start: 0.8937 (m) cc_final: 0.8717 (p) REVERT: H 110 ILE cc_start: 0.8196 (mt) cc_final: 0.7966 (mt) REVERT: L 79 GLN cc_start: 0.6849 (mm-40) cc_final: 0.6161 (mm-40) outliers start: 13 outliers final: 12 residues processed: 97 average time/residue: 0.1548 time to fit residues: 23.1159 Evaluate side-chains 95 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 0.0970 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.197526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144200 restraints weight = 9332.658| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.93 r_work: 0.3307 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8506 Z= 0.180 Angle : 0.536 9.778 11556 Z= 0.273 Chirality : 0.041 0.219 1272 Planarity : 0.004 0.042 1474 Dihedral : 4.994 53.540 1328 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.12 % Allowed : 15.12 % 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 (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: 1.38 (0.26), residues: 1022 helix: 1.98 (0.26), residues: 390 sheet: 1.56 (0.36), residues: 206 loop : -0.42 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.003 0.001 HIS L 91 PHE 0.015 0.001 PHE A 369 TYR 0.012 0.001 TYR A 385 ARG 0.005 0.000 ARG L 61 *********************** 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 97 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.828 Fit side-chains REVERT: A 133 CYS cc_start: 0.8143 (p) cc_final: 0.7293 (t) REVERT: A 394 ASN cc_start: 0.8339 (t0) cc_final: 0.8128 (m-40) REVERT: A 408 MET cc_start: 0.7801 (mmt) cc_final: 0.7522 (mmt) REVERT: H 110 ILE cc_start: 0.8160 (mt) cc_final: 0.7929 (mt) REVERT: L 79 GLN cc_start: 0.6923 (mm-40) cc_final: 0.6298 (mm-40) outliers start: 10 outliers final: 10 residues processed: 94 average time/residue: 0.1468 time to fit residues: 21.6145 Evaluate side-chains 93 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR 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: 0.7980 chunk 12 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.197094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144506 restraints weight = 9398.776| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.06 r_work: 0.3306 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8506 Z= 0.204 Angle : 0.551 9.800 11556 Z= 0.280 Chirality : 0.041 0.222 1272 Planarity : 0.004 0.041 1474 Dihedral : 5.023 52.974 1328 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.46 % Allowed : 14.89 % Favored : 83.65 % 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: 1.36 (0.26), residues: 1022 helix: 1.94 (0.26), residues: 390 sheet: 1.57 (0.36), residues: 206 loop : -0.41 (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 0.016 0.001 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.004 0.000 ARG L 61 ********************** 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 96 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.981 Fit side-chains REVERT: A 133 CYS cc_start: 0.8123 (p) cc_final: 0.7303 (t) REVERT: A 323 MET cc_start: 0.7817 (mmt) cc_final: 0.7596 (mmt) REVERT: A 394 ASN cc_start: 0.8334 (t0) cc_final: 0.8057 (m-40) REVERT: A 408 MET cc_start: 0.7694 (mmt) cc_final: 0.7457 (mmt) REVERT: H 110 ILE cc_start: 0.8181 (mt) cc_final: 0.7959 (mt) REVERT: L 78 LEU cc_start: 0.5035 (mt) cc_final: 0.4833 (mt) REVERT: L 79 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6237 (mm-40) outliers start: 13 outliers final: 11 residues processed: 93 average time/residue: 0.1964 time to fit residues: 28.1491 Evaluate side-chains 94 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 95 optimal weight: 30.0000 chunk 84 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.197744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143497 restraints weight = 9409.809| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.09 r_work: 0.3316 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8506 Z= 0.174 Angle : 0.532 9.784 11556 Z= 0.270 Chirality : 0.041 0.218 1272 Planarity : 0.004 0.041 1474 Dihedral : 4.946 53.797 1328 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.46 % Allowed : 14.56 % Favored : 83.99 % 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: 1.44 (0.27), residues: 1022 helix: 2.03 (0.26), residues: 390 sheet: 1.60 (0.37), residues: 206 loop : -0.39 (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 A 374 PHE 0.015 0.001 PHE A 369 TYR 0.024 0.001 TYR H 80 ARG 0.003 0.000 ARG L 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4122.13 seconds wall clock time: 73 minutes 31.21 seconds (4411.21 seconds total)