Starting phenix.real_space_refine on Tue Mar 3 20:15:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2s_27148/03_2026/8d2s_27148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2s_27148/03_2026/8d2s_27148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2s_27148/03_2026/8d2s_27148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2s_27148/03_2026/8d2s_27148_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2s_27148/03_2026/8d2s_27148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2s_27148/03_2026/8d2s_27148.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1605 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 36 5.16 5 Na 1 4.78 5 C 4621 2.51 5 N 1070 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7071 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3523 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 22, 'TRANS': 452} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 7, 'GLN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 475, 3523 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 22, 'TRANS': 452} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 7, 'GLN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 112 bond proxies already assigned to first conformer: 3555 Chain: "B" Number of atoms: 1423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1423 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1443 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1432 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 203, 1432 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1460 Chain: "A" Number of atoms: 623 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 43, 588 Unusual residues: {' NA': 1, 'LMT': 17, 'ZGS': 3} Classifications: {'undetermined': 21, 'water': 22} Link IDs: {None: 42} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 60 Conformer: "B" Number of residues, atoms: 43, 588 Unusual residues: {' NA': 1, 'LMT': 17, 'ZGS': 3} Classifications: {'undetermined': 21, 'water': 22} Link IDs: {None: 42} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 311 Unresolved non-hydrogen chiralities: 60 bond proxies already assigned to first conformer: 531 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AARG A 100 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 100 " occ=0.50 residue: pdb=" N AARG A 108 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 108 " occ=0.50 residue: pdb=" N AHIS A 420 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 420 " occ=0.50 residue: pdb=" N APHE A 427 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 427 " occ=0.50 residue: pdb=" N APHE A 449 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 449 " occ=0.50 residue: pdb=" N AARG C 13 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 13 " occ=0.50 residue: pdb=" C1 ALMT A 616 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 616 " occ=0.50 Time building chain proxies: 2.61, per 1000 atoms: 0.37 Number of scatterers: 7071 At special positions: 0 Unit cell: (73.428, 74.272, 142.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 3 15.00 Na 1 11.00 O 1340 8.00 N 1070 7.00 C 4621 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 353.7 milliseconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 45.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.659A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 68 removed outlier: 3.829A pdb=" N GLN A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 100 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 109 through 128 Proline residue: A 118 - end of helix removed outlier: 3.745A pdb=" N TRP A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.476A pdb=" N SER A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 200 removed outlier: 3.555A pdb=" N VAL A 185 " --> pdb=" O MET A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 232 through 262 Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 288 through 311 Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 325 through 351 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.092A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.304A pdb=" N PHE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 414 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix removed outlier: 3.536A pdb=" N ASP A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 451 removed outlier: 4.047A pdb=" N GLY A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.703A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'C' and resid 28 through 31 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.777A pdb=" N ALA B 18 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.138A pdb=" N LYS B 11 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 32 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR B 48 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.747A pdb=" N ALA B 127 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ILE B 174 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL B 129 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU B 172 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE B 131 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA B 170 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N MET B 168 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.617A pdb=" N TRP B 143 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 58 removed outlier: 7.031A pdb=" N TRP C 36 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA C 49 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL C 34 " --> pdb=" O ALA C 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91 Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.945A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 175 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.945A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AB2, first strand: chain 'C' and resid 149 through 151 removed outlier: 4.743A pdb=" N ALA C 184 " --> pdb=" O VAL C 200 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1024 1.30 - 1.43: 1895 1.43 - 1.56: 4137 1.56 - 1.68: 119 1.68 - 1.81: 51 Bond restraints: 7226 Sorted by residual: bond pdb=" C1B LMT A 611 " pdb=" O5B LMT A 611 " ideal model delta sigma weight residual 1.393 1.516 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C1BBLMT A 616 " pdb=" O5BBLMT A 616 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1B LMT A 612 " pdb=" O5B LMT A 612 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C1BALMT A 616 " pdb=" O5BALMT A 616 " ideal model delta sigma weight residual 1.393 1.512 -0.119 2.00e-02 2.50e+03 3.54e+01 ... (remaining 7221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.09: 9650 6.09 - 12.18: 133 12.18 - 18.27: 12 18.27 - 24.36: 8 24.36 - 30.45: 7 Bond angle restraints: 9810 Sorted by residual: angle pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " ideal model delta sigma weight residual 127.52 157.97 -30.45 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C09 ZGS A 601 " pdb=" C10 ZGS A 601 " pdb=" C11 ZGS A 601 " ideal model delta sigma weight residual 127.16 154.21 -27.05 3.00e+00 1.11e-01 8.13e+01 angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 110.70 137.41 -26.71 3.00e+00 1.11e-01 7.93e+01 angle pdb=" C06 ZGS A 603 " pdb=" C07 ZGS A 603 " pdb=" C08 ZGS A 603 " ideal model delta sigma weight residual 127.52 152.93 -25.41 3.00e+00 1.11e-01 7.17e+01 angle pdb=" C03 ZGS A 603 " pdb=" C04 ZGS A 603 " pdb=" C05 ZGS A 603 " ideal model delta sigma weight residual 127.34 152.52 -25.18 3.00e+00 1.11e-01 7.04e+01 ... (remaining 9805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 4343 35.93 - 71.86: 230 71.86 - 107.78: 93 107.78 - 143.71: 33 143.71 - 179.64: 4 Dihedral angle restraints: 4703 sinusoidal: 2183 harmonic: 2520 Sorted by residual: dihedral pdb=" C23 ZGS A 602 " pdb=" O24 ZGS A 602 " pdb=" P25 ZGS A 602 " pdb=" O26 ZGS A 602 " ideal model delta sinusoidal sigma weight residual 177.58 -2.06 179.64 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C23 ZGS A 603 " pdb=" O24 ZGS A 603 " pdb=" P25 ZGS A 603 " pdb=" O28 ZGS A 603 " ideal model delta sinusoidal sigma weight residual 66.18 -107.87 174.05 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C23 ZGS A 602 " pdb=" O24 ZGS A 602 " pdb=" P25 ZGS A 602 " pdb=" O28 ZGS A 602 " ideal model delta sinusoidal sigma weight residual 66.18 -125.94 -167.88 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 4700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 903 0.054 - 0.109: 194 0.109 - 0.163: 43 0.163 - 0.217: 8 0.217 - 0.271: 1 Chirality restraints: 1149 Sorted by residual: chirality pdb=" C1B LMT A 608 " pdb=" C2B LMT A 608 " pdb=" O1B LMT A 608 " pdb=" O5B LMT A 608 " both_signs ideal model delta sigma weight residual False -2.20 -2.47 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C4' LMT A 608 " pdb=" C3' LMT A 608 " pdb=" C5' LMT A 608 " pdb=" O1B LMT A 608 " both_signs ideal model delta sigma weight residual False -2.55 -2.34 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C1B LMT A 613 " pdb=" C2B LMT A 613 " pdb=" O1B LMT A 613 " pdb=" O5B LMT A 613 " both_signs ideal model delta sigma weight residual False -2.20 -2.41 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1146 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO C 47 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 431 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C PHE A 431 " -0.043 2.00e-02 2.50e+03 pdb=" O PHE A 431 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 432 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 85 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ALA A 85 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA A 85 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP A 86 " 0.011 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1998 2.82 - 3.34: 6356 3.34 - 3.86: 12101 3.86 - 4.38: 13833 4.38 - 4.90: 24264 Nonbonded interactions: 58552 Sorted by model distance: nonbonded pdb=" OG1 THR A 209 " pdb=" O HOH A 701 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR A 53 " pdb=" NE2 GLN A 152 " model vdw 2.303 3.120 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.341 3.040 nonbonded pdb=" NZ LYS A 353 " pdb=" OD2 ASP A 405 " model vdw 2.347 3.120 nonbonded pdb=" O TYR A 452 " pdb=" ND2 ASN C 99 " model vdw 2.353 3.120 ... (remaining 58547 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=0.99 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.012 0.123 7230 Z= 0.583 Angle : 1.682 30.451 9818 Z= 0.619 Chirality : 0.049 0.271 1149 Planarity : 0.006 0.070 1173 Dihedral : 27.127 179.641 3087 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.80 % Allowed : 5.91 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.27), residues: 891 helix: 0.58 (0.25), residues: 385 sheet: -0.50 (0.38), residues: 189 loop : -2.46 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 92 TYR 0.013 0.001 TYR A 251 PHE 0.016 0.002 PHE B 89 TRP 0.015 0.001 TRP A 140 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.01159 ( 7226) covalent geometry : angle 1.68301 ( 9810) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.61595 ( 8) hydrogen bonds : bond 0.12928 ( 383) hydrogen bonds : angle 6.44581 ( 1106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.278 Fit side-chains REVERT: A 106 PHE cc_start: 0.8869 (m-80) cc_final: 0.8657 (m-80) REVERT: A 132 SER cc_start: 0.8705 (p) cc_final: 0.8154 (m) REVERT: A 134 ASP cc_start: 0.6688 (p0) cc_final: 0.6457 (p0) REVERT: A 180 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7669 (ttp-170) REVERT: A 345 GLN cc_start: 0.8644 (mt0) cc_final: 0.8371 (mt0) REVERT: B 91 LYS cc_start: 0.7936 (mttt) cc_final: 0.7562 (mmtm) REVERT: B 168 MET cc_start: 0.8467 (ttt) cc_final: 0.8262 (ttp) REVERT: C 37 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7449 (mt) outliers start: 5 outliers final: 1 residues processed: 143 average time/residue: 0.4251 time to fit residues: 65.0020 Evaluate side-chains 106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 420 HIS B B 187 ASN C 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.180371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154641 restraints weight = 30958.322| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.16 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7230 Z= 0.165 Angle : 0.799 9.862 9818 Z= 0.353 Chirality : 0.046 0.302 1149 Planarity : 0.005 0.064 1173 Dihedral : 18.904 179.059 1827 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.56 % Allowed : 12.30 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.28), residues: 891 helix: 1.36 (0.26), residues: 384 sheet: -0.24 (0.39), residues: 184 loop : -2.34 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 180 TYR 0.011 0.001 TYR A 251 PHE 0.024 0.002 PHE C 38 TRP 0.017 0.002 TRP C 95 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7226) covalent geometry : angle 0.79876 ( 9810) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.53868 ( 8) hydrogen bonds : bond 0.04163 ( 383) hydrogen bonds : angle 4.92285 ( 1106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.179 Fit side-chains REVERT: A 106 PHE cc_start: 0.8865 (m-80) cc_final: 0.8629 (m-80) REVERT: A 132 SER cc_start: 0.8748 (p) cc_final: 0.8152 (m) REVERT: A 345 GLN cc_start: 0.8532 (mt0) cc_final: 0.8293 (mt0) REVERT: B 91 LYS cc_start: 0.7921 (mttt) cc_final: 0.7596 (mmtm) outliers start: 16 outliers final: 6 residues processed: 118 average time/residue: 0.4444 time to fit residues: 55.8779 Evaluate side-chains 111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 27 GLN B 187 ASN C 74 GLN C 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.177070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151545 restraints weight = 31307.501| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.94 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7230 Z= 0.196 Angle : 0.726 9.208 9818 Z= 0.342 Chirality : 0.044 0.159 1149 Planarity : 0.006 0.071 1173 Dihedral : 14.927 174.909 1825 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.56 % Allowed : 14.22 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.28), residues: 891 helix: 1.54 (0.26), residues: 384 sheet: -0.46 (0.39), residues: 191 loop : -2.39 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 31 TYR 0.014 0.002 TYR A 179 PHE 0.023 0.002 PHE C 38 TRP 0.032 0.002 TRP C 95 HIS 0.005 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 7226) covalent geometry : angle 0.72567 ( 9810) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.59022 ( 8) hydrogen bonds : bond 0.04402 ( 383) hydrogen bonds : angle 4.92388 ( 1106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.161 Fit side-chains REVERT: A 106 PHE cc_start: 0.8878 (m-80) cc_final: 0.8644 (m-80) REVERT: A 132 SER cc_start: 0.8725 (p) cc_final: 0.8159 (m) REVERT: A 431 PHE cc_start: 0.8410 (m-80) cc_final: 0.8150 (m-80) REVERT: B 91 LYS cc_start: 0.7987 (mttt) cc_final: 0.7708 (mmtm) REVERT: C 37 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7435 (mp) outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 0.4177 time to fit residues: 48.7789 Evaluate side-chains 107 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 82 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 27 GLN B 63 GLN C 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.178555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.149373 restraints weight = 35331.331| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.34 r_work: 0.3233 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7230 Z= 0.151 Angle : 0.640 8.294 9818 Z= 0.306 Chirality : 0.041 0.149 1149 Planarity : 0.005 0.068 1173 Dihedral : 13.845 168.418 1825 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.72 % Allowed : 14.22 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 891 helix: 1.71 (0.26), residues: 384 sheet: -0.40 (0.37), residues: 203 loop : -2.39 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.014 0.001 TYR A 425 PHE 0.017 0.002 PHE B 89 TRP 0.024 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7226) covalent geometry : angle 0.64018 ( 9810) SS BOND : bond 0.00099 ( 4) SS BOND : angle 0.46643 ( 8) hydrogen bonds : bond 0.03952 ( 383) hydrogen bonds : angle 4.70693 ( 1106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.240 Fit side-chains REVERT: A 106 PHE cc_start: 0.9003 (m-80) cc_final: 0.8692 (m-80) REVERT: A 132 SER cc_start: 0.9084 (p) cc_final: 0.8603 (m) REVERT: B 91 LYS cc_start: 0.8407 (mttt) cc_final: 0.8004 (mmtm) REVERT: C 37 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7723 (mp) REVERT: C 118 LYS cc_start: 0.7909 (mtpp) cc_final: 0.7595 (mtpt) outliers start: 17 outliers final: 9 residues processed: 106 average time/residue: 0.4517 time to fit residues: 50.8390 Evaluate side-chains 106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.0030 chunk 19 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.178100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.148188 restraints weight = 36051.332| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.55 r_work: 0.3206 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7230 Z= 0.153 Angle : 0.636 8.022 9818 Z= 0.306 Chirality : 0.041 0.143 1149 Planarity : 0.005 0.069 1173 Dihedral : 13.468 166.476 1825 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.88 % Allowed : 14.70 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.28), residues: 891 helix: 1.79 (0.25), residues: 384 sheet: -0.28 (0.39), residues: 187 loop : -2.35 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.014 0.002 TYR B 136 PHE 0.018 0.002 PHE B 89 TRP 0.029 0.001 TRP C 95 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 7226) covalent geometry : angle 0.63598 ( 9810) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.49277 ( 8) hydrogen bonds : bond 0.03961 ( 383) hydrogen bonds : angle 4.66279 ( 1106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.244 Fit side-chains REVERT: A 106 PHE cc_start: 0.9005 (m-80) cc_final: 0.8678 (m-80) REVERT: A 132 SER cc_start: 0.9053 (p) cc_final: 0.8594 (m) REVERT: A 431 PHE cc_start: 0.8617 (m-80) cc_final: 0.8134 (m-80) REVERT: B 91 LYS cc_start: 0.8431 (mttt) cc_final: 0.8016 (mmtm) REVERT: C 37 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7725 (mp) outliers start: 18 outliers final: 12 residues processed: 105 average time/residue: 0.4385 time to fit residues: 49.2729 Evaluate side-chains 106 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 50 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 79 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.183029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.154679 restraints weight = 36929.040| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 4.33 r_work: 0.3307 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7230 Z= 0.110 Angle : 0.579 9.353 9818 Z= 0.278 Chirality : 0.039 0.141 1149 Planarity : 0.005 0.069 1173 Dihedral : 12.513 165.461 1825 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.24 % Allowed : 15.65 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.29), residues: 891 helix: 2.08 (0.26), residues: 383 sheet: -0.23 (0.38), residues: 199 loop : -2.25 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.010 0.001 TYR A 251 PHE 0.013 0.001 PHE B 89 TRP 0.011 0.001 TRP C 95 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7226) covalent geometry : angle 0.57878 ( 9810) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.38234 ( 8) hydrogen bonds : bond 0.03562 ( 383) hydrogen bonds : angle 4.38262 ( 1106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.259 Fit side-chains REVERT: A 106 PHE cc_start: 0.8990 (m-80) cc_final: 0.8664 (m-80) REVERT: A 132 SER cc_start: 0.9044 (p) cc_final: 0.8586 (m) REVERT: A 164 MET cc_start: 0.8570 (tpp) cc_final: 0.8320 (mmp) REVERT: A 431 PHE cc_start: 0.8640 (m-80) cc_final: 0.8178 (m-80) REVERT: B 38 ARG cc_start: 0.8328 (mtt90) cc_final: 0.8090 (mpt-90) REVERT: B 91 LYS cc_start: 0.8200 (mttt) cc_final: 0.7812 (mmtm) REVERT: C 37 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7584 (mt) REVERT: C 95 TRP cc_start: 0.6885 (p-90) cc_final: 0.6384 (p-90) REVERT: C 118 LYS cc_start: 0.7741 (mtpp) cc_final: 0.7391 (mttt) outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.4449 time to fit residues: 49.9086 Evaluate side-chains 105 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.0980 chunk 76 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN C 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.178303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.150317 restraints weight = 34584.633| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.53 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7230 Z= 0.154 Angle : 0.623 8.103 9818 Z= 0.303 Chirality : 0.041 0.143 1149 Planarity : 0.005 0.069 1173 Dihedral : 12.424 165.827 1825 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.76 % Allowed : 16.77 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.28), residues: 891 helix: 2.06 (0.26), residues: 383 sheet: -0.23 (0.41), residues: 175 loop : -2.25 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.014 0.002 TYR A 425 PHE 0.020 0.002 PHE B 89 TRP 0.030 0.001 TRP C 95 HIS 0.004 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7226) covalent geometry : angle 0.62268 ( 9810) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.46122 ( 8) hydrogen bonds : bond 0.03882 ( 383) hydrogen bonds : angle 4.52198 ( 1106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.233 Fit side-chains REVERT: A 106 PHE cc_start: 0.8973 (m-80) cc_final: 0.8699 (m-80) REVERT: A 132 SER cc_start: 0.8763 (p) cc_final: 0.8199 (m) REVERT: A 180 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7708 (ttt90) REVERT: A 431 PHE cc_start: 0.8481 (m-80) cc_final: 0.8173 (m-80) REVERT: B 91 LYS cc_start: 0.7899 (mttt) cc_final: 0.7632 (mmtm) REVERT: C 37 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7283 (mt) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.4458 time to fit residues: 46.5513 Evaluate side-chains 100 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 50 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.179363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151452 restraints weight = 28410.848| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.46 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7230 Z= 0.139 Angle : 0.607 7.944 9818 Z= 0.294 Chirality : 0.041 0.142 1149 Planarity : 0.005 0.070 1173 Dihedral : 12.235 165.708 1825 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.08 % Allowed : 16.13 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.29), residues: 891 helix: 2.11 (0.26), residues: 383 sheet: -0.22 (0.38), residues: 197 loop : -2.25 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.015 0.001 TYR B 136 PHE 0.016 0.002 PHE B 89 TRP 0.026 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7226) covalent geometry : angle 0.60676 ( 9810) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.43763 ( 8) hydrogen bonds : bond 0.03785 ( 383) hydrogen bonds : angle 4.47662 ( 1106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.191 Fit side-chains REVERT: A 106 PHE cc_start: 0.8965 (m-80) cc_final: 0.8696 (m-80) REVERT: A 132 SER cc_start: 0.8723 (p) cc_final: 0.8134 (m) REVERT: A 134 ASP cc_start: 0.6862 (p0) cc_final: 0.6452 (p0) REVERT: A 431 PHE cc_start: 0.8415 (m-80) cc_final: 0.8125 (m-80) REVERT: B 91 LYS cc_start: 0.7875 (mttt) cc_final: 0.7622 (mmtm) REVERT: C 37 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7311 (mp) outliers start: 13 outliers final: 9 residues processed: 95 average time/residue: 0.4497 time to fit residues: 45.5442 Evaluate side-chains 99 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 71 optimal weight: 0.0010 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 34 optimal weight: 0.0010 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.181969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.154374 restraints weight = 35104.746| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.50 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7230 Z= 0.116 Angle : 0.568 7.608 9818 Z= 0.276 Chirality : 0.039 0.144 1149 Planarity : 0.005 0.070 1173 Dihedral : 11.665 166.585 1825 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.76 % Allowed : 16.61 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.29), residues: 891 helix: 2.23 (0.26), residues: 383 sheet: -0.17 (0.38), residues: 199 loop : -2.17 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.013 0.001 TYR B 136 PHE 0.014 0.001 PHE B 89 TRP 0.016 0.001 TRP C 95 HIS 0.002 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7226) covalent geometry : angle 0.56817 ( 9810) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.37567 ( 8) hydrogen bonds : bond 0.03557 ( 383) hydrogen bonds : angle 4.33561 ( 1106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.156 Fit side-chains REVERT: A 106 PHE cc_start: 0.8909 (m-80) cc_final: 0.8625 (m-80) REVERT: A 110 MET cc_start: 0.8332 (mmt) cc_final: 0.8022 (mmt) REVERT: A 132 SER cc_start: 0.8694 (p) cc_final: 0.8104 (m) REVERT: A 180 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7934 (ttt-90) REVERT: B 154 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7504 (mtp) REVERT: B 168 MET cc_start: 0.8553 (ttt) cc_final: 0.8331 (ttp) REVERT: C 37 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7266 (mp) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.4649 time to fit residues: 49.1038 Evaluate side-chains 103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN B 142 GLN C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.178224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150961 restraints weight = 32882.867| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.26 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7230 Z= 0.151 Angle : 0.614 7.768 9818 Z= 0.300 Chirality : 0.041 0.165 1149 Planarity : 0.005 0.069 1173 Dihedral : 11.649 165.661 1825 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.60 % Allowed : 17.09 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.29), residues: 891 helix: 2.15 (0.26), residues: 383 sheet: -0.15 (0.42), residues: 175 loop : -2.20 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.017 0.002 TYR B 136 PHE 0.017 0.002 PHE B 89 TRP 0.028 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7226) covalent geometry : angle 0.61401 ( 9810) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.46326 ( 8) hydrogen bonds : bond 0.03854 ( 383) hydrogen bonds : angle 4.46534 ( 1106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.245 Fit side-chains REVERT: A 106 PHE cc_start: 0.8904 (m-80) cc_final: 0.8671 (m-80) REVERT: A 132 SER cc_start: 0.8730 (p) cc_final: 0.8118 (m) REVERT: A 134 ASP cc_start: 0.6803 (p0) cc_final: 0.6465 (p0) REVERT: B 63 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: B 168 MET cc_start: 0.8645 (ttt) cc_final: 0.8410 (ttp) REVERT: C 37 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7289 (mt) outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.4621 time to fit residues: 47.7008 Evaluate side-chains 99 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN B 142 GLN C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.178314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.150591 restraints weight = 25950.769| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.29 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 7230 Z= 0.216 Angle : 1.042 59.199 9818 Z= 0.580 Chirality : 0.042 0.373 1149 Planarity : 0.005 0.070 1173 Dihedral : 11.648 165.661 1825 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.24 % Allowed : 16.45 % Favored : 81.31 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.29), residues: 891 helix: 2.16 (0.26), residues: 383 sheet: -0.13 (0.41), residues: 180 loop : -2.24 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.017 0.002 TYR B 136 PHE 0.017 0.002 PHE B 89 TRP 0.032 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 7226) covalent geometry : angle 1.04225 ( 9810) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.45641 ( 8) hydrogen bonds : bond 0.03961 ( 383) hydrogen bonds : angle 4.47569 ( 1106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.47 seconds wall clock time: 35 minutes 26.38 seconds (2126.38 seconds total)