Starting phenix.real_space_refine on Sat Jul 26 10:17:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2s_27148/07_2025/8d2s_27148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2s_27148/07_2025/8d2s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2s_27148/07_2025/8d2s_27148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2s_27148/07_2025/8d2s_27148.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2s_27148/07_2025/8d2s_27148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2s_27148/07_2025/8d2s_27148_neut.cif" } resolution = 2.9 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= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6} 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: {'GLN:plan1': 6, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 6} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, '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: 7.80, per 1000 atoms: 1.10 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: 2.09 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.86 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: 2.03 Time building geometry restraints manager: 2.30 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.000 ------------------------------------------------------------------------------- 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 : 6.89 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 (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: -1.07 (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 TRP 0.015 0.001 TRP A 140 HIS 0.005 0.001 HIS A 156 PHE 0.016 0.002 PHE B 89 TYR 0.013 0.001 TYR A 251 ARG 0.002 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.12928 ( 383) hydrogen bonds : angle 6.44581 ( 1106) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.61595 ( 8) covalent geometry : bond 0.01159 ( 7226) covalent geometry : angle 1.68301 ( 9810) *********************** 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 : 0.699 Fit side-chains REVERT: A 106 PHE cc_start: 0.8869 (m-80) cc_final: 0.8656 (m-80) REVERT: A 132 SER cc_start: 0.8705 (p) cc_final: 0.8156 (m) REVERT: A 134 ASP cc_start: 0.6688 (p0) cc_final: 0.6453 (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: 0.7563 (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: 0.9278 time to fit residues: 141.7829 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 : 0.725 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.176865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.146775 restraints weight = 38587.386| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.38 r_work: 0.3193 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7230 Z= 0.206 Angle : 0.846 9.820 9818 Z= 0.380 Chirality : 0.049 0.325 1149 Planarity : 0.006 0.066 1173 Dihedral : 19.325 177.935 1827 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.04 % Allowed : 12.14 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.28), residues: 891 helix: 1.24 (0.26), residues: 384 sheet: -0.28 (0.39), residues: 184 loop : -2.39 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 95 HIS 0.003 0.001 HIS A 156 PHE 0.028 0.003 PHE C 38 TYR 0.012 0.002 TYR A 251 ARG 0.004 0.001 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 383) hydrogen bonds : angle 5.10073 ( 1106) SS BOND : bond 0.00278 ( 4) SS BOND : angle 0.65580 ( 8) covalent geometry : bond 0.00481 ( 7226) covalent geometry : angle 0.84655 ( 9810) *********************** 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 131 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.689 Fit side-chains REVERT: A 106 PHE cc_start: 0.9062 (m-80) cc_final: 0.8685 (m-80) REVERT: A 132 SER cc_start: 0.9140 (p) cc_final: 0.8677 (m) REVERT: A 345 GLN cc_start: 0.8572 (mt0) cc_final: 0.8150 (mt0) REVERT: B 91 LYS cc_start: 0.8461 (mttt) cc_final: 0.8037 (mmtm) REVERT: C 19 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8953 (tp40) REVERT: C 188 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7900 (t) outliers start: 19 outliers final: 7 residues processed: 116 average time/residue: 0.9484 time to fit residues: 117.6503 Evaluate side-chains 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 88 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 188 VAL 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 49 optimal weight: 0.0000 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 44 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 63 GLN B 187 ASN C 19 GLN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.179193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.153396 restraints weight = 30078.827| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.04 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7230 Z= 0.151 Angle : 0.676 7.862 9818 Z= 0.316 Chirality : 0.042 0.158 1149 Planarity : 0.005 0.067 1173 Dihedral : 15.235 175.440 1825 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.72 % Allowed : 13.42 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.28), residues: 891 helix: 1.59 (0.26), residues: 382 sheet: -0.43 (0.38), residues: 198 loop : -2.41 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 PHE 0.017 0.002 PHE B 89 TYR 0.012 0.001 TYR A 425 ARG 0.003 0.001 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 383) hydrogen bonds : angle 4.83863 ( 1106) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.50363 ( 8) covalent geometry : bond 0.00346 ( 7226) covalent geometry : angle 0.67584 ( 9810) *********************** 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 128 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.594 Fit side-chains REVERT: A 106 PHE cc_start: 0.8887 (m-80) cc_final: 0.8611 (m-80) REVERT: A 132 SER cc_start: 0.8716 (p) cc_final: 0.8123 (m) REVERT: B 27 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6996 (tm130) REVERT: B 91 LYS cc_start: 0.7973 (mttt) cc_final: 0.7709 (mmtm) REVERT: C 37 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7394 (mp) outliers start: 17 outliers final: 11 residues processed: 118 average time/residue: 0.9664 time to fit residues: 122.5079 Evaluate side-chains 117 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 27 GLN 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 174 SER Chi-restraints excluded: chain C residue 179 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 82 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 19 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 = 0.3919 r_free = 0.3919 target = 0.175395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.146224 restraints weight = 34585.796| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 4.09 r_work: 0.3163 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7230 Z= 0.204 Angle : 0.708 9.506 9818 Z= 0.340 Chirality : 0.044 0.162 1149 Planarity : 0.005 0.071 1173 Dihedral : 14.463 170.151 1825 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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 (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: -0.38 (0.28), residues: 891 helix: 1.54 (0.25), residues: 384 sheet: -0.44 (0.38), residues: 187 loop : -2.45 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 95 HIS 0.006 0.001 HIS A 156 PHE 0.029 0.002 PHE A 431 TYR 0.015 0.002 TYR B 136 ARG 0.008 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 383) hydrogen bonds : angle 4.89626 ( 1106) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.64569 ( 8) covalent geometry : bond 0.00489 ( 7226) covalent geometry : angle 0.70830 ( 9810) *********************** 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 119 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.696 Fit side-chains REVERT: A 106 PHE cc_start: 0.9013 (m-80) cc_final: 0.8689 (m-80) REVERT: A 132 SER cc_start: 0.9092 (p) cc_final: 0.8612 (m) REVERT: B 91 LYS cc_start: 0.8452 (mttt) cc_final: 0.8027 (mmtm) REVERT: C 37 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7778 (mp) outliers start: 17 outliers final: 10 residues processed: 109 average time/residue: 0.9024 time to fit residues: 105.5455 Evaluate side-chains 109 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 B residue 67 THR Chi-restraints excluded: chain B residue 88 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 185 THR 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 1 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.0470 chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 63 GLN C 19 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 = 0.3947 r_free = 0.3947 target = 0.178135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.152071 restraints weight = 31141.754| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.11 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7230 Z= 0.146 Angle : 0.629 7.642 9818 Z= 0.303 Chirality : 0.041 0.141 1149 Planarity : 0.005 0.069 1173 Dihedral : 13.537 166.166 1825 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.51 % Allowed : 14.38 % 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 (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: -0.17 (0.28), residues: 891 helix: 1.80 (0.26), residues: 382 sheet: -0.38 (0.39), residues: 187 loop : -2.39 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 PHE 0.016 0.002 PHE B 89 TYR 0.013 0.001 TYR A 425 ARG 0.007 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 383) hydrogen bonds : angle 4.68459 ( 1106) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.52383 ( 8) covalent geometry : bond 0.00340 ( 7226) covalent geometry : angle 0.62882 ( 9810) *********************** 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 123 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.658 Fit side-chains REVERT: A 106 PHE cc_start: 0.8893 (m-80) cc_final: 0.8660 (m-80) REVERT: A 132 SER cc_start: 0.8726 (p) cc_final: 0.8109 (m) REVERT: A 431 PHE cc_start: 0.8329 (m-80) cc_final: 0.8046 (m-80) REVERT: B 63 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: B 91 LYS cc_start: 0.7854 (mttt) cc_final: 0.7642 (mmtm) REVERT: C 37 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7396 (mp) outliers start: 22 outliers final: 10 residues processed: 112 average time/residue: 0.9203 time to fit residues: 110.5910 Evaluate side-chains 108 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 19 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 = 0.3923 r_free = 0.3923 target = 0.175683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147655 restraints weight = 29755.643| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.43 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7230 Z= 0.183 Angle : 0.666 8.795 9818 Z= 0.322 Chirality : 0.042 0.145 1149 Planarity : 0.005 0.071 1173 Dihedral : 13.453 164.616 1825 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.04 % Allowed : 15.34 % 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 (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: -0.14 (0.28), residues: 891 helix: 1.78 (0.25), residues: 384 sheet: -0.35 (0.39), residues: 187 loop : -2.36 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 95 HIS 0.005 0.001 HIS A 156 PHE 0.020 0.002 PHE B 89 TYR 0.016 0.002 TYR B 136 ARG 0.004 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 383) hydrogen bonds : angle 4.74459 ( 1106) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.57534 ( 8) covalent geometry : bond 0.00439 ( 7226) covalent geometry : angle 0.66570 ( 9810) *********************** 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 119 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.635 Fit side-chains REVERT: A 106 PHE cc_start: 0.8989 (m-80) cc_final: 0.8711 (m-80) REVERT: A 132 SER cc_start: 0.8792 (p) cc_final: 0.8206 (m) REVERT: A 134 ASP cc_start: 0.6932 (p0) cc_final: 0.6561 (p0) REVERT: A 264 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: A 431 PHE cc_start: 0.8357 (m-80) cc_final: 0.8044 (m-80) REVERT: B 91 LYS cc_start: 0.7991 (mttt) cc_final: 0.7681 (mmtm) REVERT: C 37 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7431 (mp) REVERT: C 78 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7743 (mp0) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 0.9701 time to fit residues: 112.7988 Evaluate side-chains 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU 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 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 78 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 81 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN C 19 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 = 0.3949 r_free = 0.3949 target = 0.178167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.148927 restraints weight = 37265.205| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 4.01 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2451 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= 0.136 Angle : 0.620 8.236 9818 Z= 0.299 Chirality : 0.041 0.137 1149 Planarity : 0.005 0.071 1173 Dihedral : 12.974 164.164 1825 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.40 % Allowed : 16.13 % 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 (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: 0.03 (0.28), residues: 891 helix: 1.96 (0.26), residues: 384 sheet: -0.41 (0.37), residues: 203 loop : -2.30 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 PHE 0.015 0.002 PHE B 89 TYR 0.014 0.001 TYR B 136 ARG 0.009 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 383) hydrogen bonds : angle 4.59791 ( 1106) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.43965 ( 8) covalent geometry : bond 0.00314 ( 7226) covalent geometry : angle 0.62053 ( 9810) *********************** 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 111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.702 Fit side-chains REVERT: A 106 PHE cc_start: 0.8982 (m-80) cc_final: 0.8717 (m-80) REVERT: A 132 SER cc_start: 0.8744 (p) cc_final: 0.8164 (m) REVERT: A 264 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: A 431 PHE cc_start: 0.8493 (m-80) cc_final: 0.8161 (m-80) REVERT: B 91 LYS cc_start: 0.7918 (mttt) cc_final: 0.7648 (mmtm) REVERT: C 37 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7381 (mp) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 1.1048 time to fit residues: 122.3907 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 : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 406 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.2980 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 19 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 = 0.3945 r_free = 0.3945 target = 0.177872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.151259 restraints weight = 31605.032| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.14 r_work: 0.3247 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7230 Z= 0.146 Angle : 0.620 7.900 9818 Z= 0.301 Chirality : 0.041 0.143 1149 Planarity : 0.005 0.071 1173 Dihedral : 12.548 163.882 1825 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.56 % Allowed : 15.97 % 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 (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: 0.05 (0.28), residues: 891 helix: 1.98 (0.26), residues: 385 sheet: -0.30 (0.39), residues: 187 loop : -2.30 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 PHE 0.017 0.002 PHE B 89 TYR 0.015 0.002 TYR A 425 ARG 0.008 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 383) hydrogen bonds : angle 4.56509 ( 1106) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.47462 ( 8) covalent geometry : bond 0.00342 ( 7226) covalent geometry : angle 0.62003 ( 9810) *********************** 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 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.690 Fit side-chains REVERT: A 106 PHE cc_start: 0.9041 (m-80) cc_final: 0.8745 (m-80) REVERT: A 110 MET cc_start: 0.8635 (mmt) cc_final: 0.8243 (mmt) REVERT: A 132 SER cc_start: 0.9105 (p) cc_final: 0.8635 (m) REVERT: A 134 ASP cc_start: 0.7608 (p0) cc_final: 0.7217 (p0) REVERT: A 264 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: A 431 PHE cc_start: 0.8722 (m-80) cc_final: 0.8318 (m-80) REVERT: B 63 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: B 91 LYS cc_start: 0.8243 (mttt) cc_final: 0.7927 (mmtm) REVERT: C 37 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7688 (mt) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 1.2467 time to fit residues: 138.6098 Evaluate side-chains 111 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU 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 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 141 VAL 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 67 optimal weight: 0.0770 chunk 79 optimal weight: 0.0030 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 13 optimal weight: 0.0470 chunk 76 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.0670 overall best weight: 0.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 GLN C 19 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 = 0.4015 r_free = 0.4015 target = 0.184865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.159165 restraints weight = 33001.748| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.20 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3720 r_free = 0.3720 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 7230 Z= 0.106 Angle : 0.570 8.788 9818 Z= 0.277 Chirality : 0.039 0.139 1149 Planarity : 0.005 0.071 1173 Dihedral : 11.823 165.506 1825 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.08 % Allowed : 16.61 % 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 (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: 0.30 (0.29), residues: 891 helix: 2.22 (0.26), residues: 384 sheet: -0.29 (0.38), residues: 199 loop : -2.19 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 400 HIS 0.001 0.000 HIS A 288 PHE 0.014 0.001 PHE C 38 TYR 0.012 0.001 TYR A 425 ARG 0.009 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 383) hydrogen bonds : angle 4.35163 ( 1106) SS BOND : bond 0.00251 ( 4) SS BOND : angle 0.36558 ( 8) covalent geometry : bond 0.00227 ( 7226) covalent geometry : angle 0.57050 ( 9810) *********************** 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 113 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.834 Fit side-chains REVERT: A 106 PHE cc_start: 0.8890 (m-80) cc_final: 0.8630 (m-80) REVERT: A 132 SER cc_start: 0.8672 (p) cc_final: 0.8039 (m) REVERT: A 180 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7847 (ttt90) REVERT: A 264 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: A 431 PHE cc_start: 0.8453 (m-80) cc_final: 0.8214 (m-80) REVERT: B 168 MET cc_start: 0.8564 (ttt) cc_final: 0.8307 (ttp) REVERT: C 61 ARG cc_start: 0.7858 (ttt90) cc_final: 0.7647 (ttt180) outliers start: 13 outliers final: 6 residues processed: 107 average time/residue: 1.2421 time to fit residues: 142.4936 Evaluate side-chains 103 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU 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 141 VAL 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 45 optimal weight: 0.0070 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 0.0370 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 142 GLN B 187 ASN C 19 GLN C 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.180443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.153120 restraints weight = 33463.797| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.35 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7230 Z= 0.138 Angle : 0.605 8.727 9818 Z= 0.294 Chirality : 0.041 0.141 1149 Planarity : 0.005 0.069 1173 Dihedral : 11.781 165.246 1825 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.44 % Allowed : 18.37 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.29), residues: 891 helix: 2.21 (0.26), residues: 383 sheet: -0.34 (0.38), residues: 200 loop : -2.14 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 95 HIS 0.003 0.001 HIS A 156 PHE 0.017 0.002 PHE B 89 TYR 0.017 0.002 TYR A 425 ARG 0.010 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 383) hydrogen bonds : angle 4.44544 ( 1106) SS BOND : bond 0.00244 ( 4) SS BOND : angle 0.54715 ( 8) covalent geometry : bond 0.00324 ( 7226) covalent geometry : angle 0.60490 ( 9810) ********************** 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 104 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.690 Fit side-chains REVERT: A 106 PHE cc_start: 0.8925 (m-80) cc_final: 0.8688 (m-80) REVERT: A 132 SER cc_start: 0.8668 (p) cc_final: 0.8081 (m) REVERT: A 180 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7869 (ttt90) REVERT: A 264 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6872 (mt-10) REVERT: A 431 PHE cc_start: 0.8465 (m-80) cc_final: 0.8213 (m-80) REVERT: C 37 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7343 (mp) REVERT: C 61 ARG cc_start: 0.7884 (ttt90) cc_final: 0.7677 (ttt180) outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 1.3396 time to fit residues: 142.6192 Evaluate side-chains 99 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain C residue 37 LEU 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 58 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 142 GLN B 187 ASN C 19 GLN C 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.175908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.148168 restraints weight = 34593.622| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.42 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7230 Z= 0.180 Angle : 0.662 8.671 9818 Z= 0.323 Chirality : 0.042 0.147 1149 Planarity : 0.005 0.069 1173 Dihedral : 12.023 163.489 1825 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.76 % Allowed : 17.89 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.28), residues: 891 helix: 2.06 (0.26), residues: 383 sheet: -0.29 (0.41), residues: 174 loop : -2.18 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 95 HIS 0.004 0.001 HIS A 156 PHE 0.020 0.002 PHE B 89 TYR 0.021 0.002 TYR A 425 ARG 0.010 0.001 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 383) hydrogen bonds : angle 4.64317 ( 1106) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.57269 ( 8) covalent geometry : bond 0.00435 ( 7226) covalent geometry : angle 0.66183 ( 9810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6969.92 seconds wall clock time: 126 minutes 11.81 seconds (7571.81 seconds total)