Starting phenix.real_space_refine on Fri Oct 10 16:57:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1m_41817/10_2025/8u1m_41817.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1m_41817/10_2025/8u1m_41817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u1m_41817/10_2025/8u1m_41817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1m_41817/10_2025/8u1m_41817.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u1m_41817/10_2025/8u1m_41817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1m_41817/10_2025/8u1m_41817.map" } resolution = 3.5 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 4988 2.51 5 N 1318 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7882 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3789 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 10, 'TRANS': 452} Chain breaks: 2 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4029 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 11, 'TRANS': 482} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.74, per 1000 atoms: 0.22 Number of scatterers: 7882 At special positions: 0 Unit cell: (90.948, 110.682, 108.108, 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 28 16.00 P 6 15.00 Mg 2 11.99 O 1540 8.00 N 1318 7.00 C 4988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.49 Conformation dependent library (CDL) restraints added in 320.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 40.1% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.849A pdb=" N MET A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 61 removed outlier: 4.083A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.790A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.586A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.570A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.853A pdb=" N LEU A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 443 removed outlier: 6.932A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.747A pdb=" N ALA A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 474 Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'B' and resid 20 through 32 removed outlier: 4.353A pdb=" N SER B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 60 removed outlier: 4.018A pdb=" N ARG B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR B 60 " --> pdb=" O TYR B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.115A pdb=" N ALA B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 removed outlier: 3.633A pdb=" N TYR B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 138 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.912A pdb=" N LEU B 342 " --> pdb=" O PRO B 339 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 343 " --> pdb=" O PHE B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 339 through 343' Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.244A pdb=" N LEU B 368 " --> pdb=" O ASN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 396 through 421 removed outlier: 3.887A pdb=" N GLU B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 443 removed outlier: 6.599A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 454 Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.920A pdb=" N VAL B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.873A pdb=" N ARG B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.690A pdb=" N VAL B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 4.326A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 278 removed outlier: 6.674A pdb=" N ILE A 73 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N THR A 216 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE A 75 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU A 218 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 85 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 179 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 143 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 147 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 168 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 13 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.794A pdb=" N ILE A 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 322 removed outlier: 6.351A pdb=" N VAL A 334 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 317 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A 319 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA A 330 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER A 321 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 328 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 380 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 382 " --> pdb=" O TYR A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AA7, first strand: chain 'B' and resid 316 through 322 removed outlier: 4.413A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 320 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 377 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AA9, first strand: chain 'B' and resid 510 through 512 removed outlier: 7.449A pdb=" N TYR B 483 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N MET B 512 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 485 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 482 " --> pdb=" O VAL B 533 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 849 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: 1.06 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2483 1.34 - 1.45: 1081 1.45 - 1.57: 4405 1.57 - 1.69: 4 1.69 - 1.81: 48 Bond restraints: 8021 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.217 0.226 1.00e-02 1.00e+04 5.12e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.92e+02 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.370 0.053 1.10e-02 8.26e+03 2.36e+01 bond pdb=" C4' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.81e+01 bond pdb=" C1' ATP B 801 " pdb=" O4' ATP B 801 " ideal model delta sigma weight residual 1.416 1.361 0.055 1.30e-02 5.92e+03 1.79e+01 ... (remaining 8016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.86: 10764 6.86 - 13.73: 19 13.73 - 20.59: 4 20.59 - 27.45: 0 27.45 - 34.32: 8 Bond angle restraints: 10795 Sorted by residual: angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 155.59 -34.32 1.00e+00 1.00e+00 1.18e+03 angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.25 -33.98 1.00e+00 1.00e+00 1.15e+03 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 83.50 31.69 1.76e+00 3.23e-01 3.24e+02 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 84.32 30.87 1.76e+00 3.23e-01 3.08e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 140.19 -31.36 2.33e+00 1.85e-01 1.82e+02 ... (remaining 10790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4276 17.98 - 35.95: 516 35.95 - 53.93: 112 53.93 - 71.91: 22 71.91 - 89.88: 10 Dihedral angle restraints: 4936 sinusoidal: 2122 harmonic: 2814 Sorted by residual: dihedral pdb=" CA MET B 512 " pdb=" C MET B 512 " pdb=" N THR B 513 " pdb=" CA THR B 513 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA MET A 25 " pdb=" C MET A 25 " pdb=" N SER A 26 " pdb=" CA SER A 26 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR A 456 " pdb=" C TYR A 456 " pdb=" N HIS A 457 " pdb=" CA HIS A 457 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1117 0.094 - 0.188: 52 0.188 - 0.282: 4 0.282 - 0.376: 0 0.376 - 0.471: 2 Chirality restraints: 1175 Sorted by residual: chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.96 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.96 0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C3' ATP A 801 " pdb=" C2' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" O3' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1172 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 311 " -0.014 2.00e-02 2.50e+03 1.70e-02 7.19e+00 pdb=" CG TRP A 311 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 311 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 311 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 311 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 311 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 311 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 311 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 211 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 212 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " -0.136 9.50e-02 1.11e+02 6.11e-02 2.39e+00 pdb=" NE ARG A 177 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " -0.007 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 69 2.40 - 3.03: 4825 3.03 - 3.65: 13142 3.65 - 4.28: 19190 4.28 - 4.90: 29932 Nonbonded interactions: 67158 Sorted by model distance: nonbonded pdb=" CB SER B 159 " pdb=" CD1 PHE B 165 " model vdw 1.781 3.740 nonbonded pdb=" O2G ATP A 801 " pdb="MG MG A 802 " model vdw 1.938 2.170 nonbonded pdb=" O3A ATP B 801 " pdb="MG MG B 802 " model vdw 1.967 2.170 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 1.971 2.170 nonbonded pdb=" O2A ATP A 801 " pdb="MG MG A 802 " model vdw 2.028 2.170 ... (remaining 67153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 10 through 490 or resid 507 through 530 or resid 801 throu \ gh 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.490 Find NCS groups from input model: 0.070 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.005 0.226 8021 Z= 0.425 Angle : 1.167 34.316 10795 Z= 0.717 Chirality : 0.048 0.471 1175 Planarity : 0.004 0.061 1374 Dihedral : 16.519 89.885 3122 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.35 % Allowed : 18.79 % Favored : 80.86 % 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 aren not related in a simple way. whole: -1.18 (0.27), residues: 947 helix: 0.01 (0.30), residues: 313 sheet: -1.23 (0.42), residues: 156 loop : -1.10 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 177 TYR 0.015 0.002 TYR A 372 PHE 0.010 0.001 PHE A 208 TRP 0.046 0.003 TRP A 311 HIS 0.007 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 8021) covalent geometry : angle 1.16714 (10795) hydrogen bonds : bond 0.22434 ( 316) hydrogen bonds : angle 9.26347 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.5009 (mmt) cc_final: 0.4370 (mmt) REVERT: B 362 MET cc_start: 0.4810 (tpt) cc_final: 0.4181 (tpp) REVERT: B 475 MET cc_start: 0.4829 (mtm) cc_final: 0.4611 (ptp) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.0974 time to fit residues: 5.1069 Evaluate side-chains 31 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 40.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 ASN B 118 GLN B 150 ASN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN B 431 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.042470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.034647 restraints weight = 94801.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.035421 restraints weight = 68004.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.035966 restraints weight = 53545.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.036352 restraints weight = 44855.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.036620 restraints weight = 39334.030| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8021 Z= 0.179 Angle : 0.637 6.977 10795 Z= 0.344 Chirality : 0.043 0.165 1175 Planarity : 0.004 0.043 1374 Dihedral : 10.467 89.816 1110 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.32 % Allowed : 17.87 % Favored : 79.81 % 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 aren not related in a simple way. whole: -1.30 (0.27), residues: 947 helix: 0.06 (0.30), residues: 326 sheet: -1.41 (0.40), residues: 160 loop : -1.27 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 177 TYR 0.015 0.002 TYR B 519 PHE 0.010 0.001 PHE A 208 TRP 0.017 0.002 TRP A 311 HIS 0.008 0.002 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8021) covalent geometry : angle 0.63739 (10795) hydrogen bonds : bond 0.04744 ( 316) hydrogen bonds : angle 7.25991 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8731 (ppp) cc_final: 0.8466 (ppp) REVERT: B 362 MET cc_start: 0.5562 (tpt) cc_final: 0.4321 (tpp) outliers start: 20 outliers final: 10 residues processed: 49 average time/residue: 0.0650 time to fit residues: 4.9114 Evaluate side-chains 40 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 75 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.044354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.036503 restraints weight = 89920.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.037366 restraints weight = 63410.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.037960 restraints weight = 49139.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.038402 restraints weight = 40616.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.038708 restraints weight = 35178.250| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8021 Z= 0.105 Angle : 0.543 6.893 10795 Z= 0.295 Chirality : 0.042 0.165 1175 Planarity : 0.003 0.035 1374 Dihedral : 9.765 83.571 1110 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.90 % Allowed : 16.47 % Favored : 80.63 % 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 aren not related in a simple way. whole: -1.15 (0.27), residues: 947 helix: 0.27 (0.30), residues: 321 sheet: -1.42 (0.41), residues: 162 loop : -1.20 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 348 TYR 0.019 0.001 TYR A 372 PHE 0.009 0.001 PHE B 303 TRP 0.020 0.002 TRP A 311 HIS 0.006 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 8021) covalent geometry : angle 0.54267 (10795) hydrogen bonds : bond 0.03680 ( 316) hydrogen bonds : angle 6.56459 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 31 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 362 MET cc_start: 0.5285 (tpt) cc_final: 0.4250 (tpp) REVERT: B 421 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8804 (p0) outliers start: 25 outliers final: 9 residues processed: 55 average time/residue: 0.0736 time to fit residues: 6.2904 Evaluate side-chains 42 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 40.0000 chunk 14 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 128 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 406 ASN B 479 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.040593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.032821 restraints weight = 99709.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.033543 restraints weight = 72117.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.034068 restraints weight = 57383.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.034456 restraints weight = 48366.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.034727 restraints weight = 42468.171| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8021 Z= 0.288 Angle : 0.774 12.382 10795 Z= 0.402 Chirality : 0.045 0.144 1175 Planarity : 0.005 0.062 1374 Dihedral : 10.687 89.243 1110 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 27.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.87 % Allowed : 16.59 % Favored : 78.54 % 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 aren not related in a simple way. whole: -1.49 (0.26), residues: 947 helix: -0.00 (0.29), residues: 316 sheet: -1.68 (0.40), residues: 165 loop : -1.36 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 177 TYR 0.018 0.003 TYR A 300 PHE 0.014 0.002 PHE A 84 TRP 0.018 0.003 TRP A 311 HIS 0.007 0.002 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 8021) covalent geometry : angle 0.77430 (10795) hydrogen bonds : bond 0.04651 ( 316) hydrogen bonds : angle 6.85596 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 32 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8676 (ppp) cc_final: 0.8294 (ppp) REVERT: B 24 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9142 (mt) REVERT: B 84 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7246 (t80) REVERT: B 128 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: B 156 MET cc_start: 0.4982 (tpp) cc_final: 0.4767 (mmm) REVERT: B 300 TYR cc_start: 0.2302 (OUTLIER) cc_final: 0.1916 (m-10) REVERT: B 421 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8988 (p0) REVERT: B 512 MET cc_start: 0.5913 (ppp) cc_final: 0.5628 (ppp) outliers start: 42 outliers final: 21 residues processed: 70 average time/residue: 0.0740 time to fit residues: 7.5424 Evaluate side-chains 57 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 31 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.042108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.034242 restraints weight = 96296.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.035021 restraints weight = 69569.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.035557 restraints weight = 54940.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.035947 restraints weight = 46280.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.036224 restraints weight = 40726.716| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8021 Z= 0.142 Angle : 0.630 12.614 10795 Z= 0.326 Chirality : 0.042 0.155 1175 Planarity : 0.003 0.051 1374 Dihedral : 9.909 87.494 1110 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.60 % Allowed : 18.21 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.27), residues: 947 helix: 0.20 (0.30), residues: 320 sheet: -1.75 (0.39), residues: 168 loop : -1.38 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.018 0.002 TYR A 372 PHE 0.019 0.001 PHE B 333 TRP 0.027 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8021) covalent geometry : angle 0.63044 (10795) hydrogen bonds : bond 0.03721 ( 316) hydrogen bonds : angle 6.57722 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 32 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8740 (ppp) cc_final: 0.8372 (ppp) REVERT: B 156 MET cc_start: 0.4721 (tpp) cc_final: 0.4481 (mmm) REVERT: B 421 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.9027 (p0) REVERT: B 512 MET cc_start: 0.5735 (ppp) cc_final: 0.5508 (ppp) outliers start: 31 outliers final: 23 residues processed: 59 average time/residue: 0.0842 time to fit residues: 7.3254 Evaluate side-chains 55 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 64 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.042157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.034278 restraints weight = 94642.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.035045 restraints weight = 68563.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.035584 restraints weight = 54556.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.035964 restraints weight = 46051.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.036223 restraints weight = 40591.282| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8021 Z= 0.139 Angle : 0.611 9.685 10795 Z= 0.315 Chirality : 0.042 0.161 1175 Planarity : 0.003 0.043 1374 Dihedral : 9.809 86.934 1110 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.29 % Allowed : 17.75 % Favored : 77.96 % 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 aren not related in a simple way. whole: -1.31 (0.27), residues: 947 helix: 0.32 (0.30), residues: 320 sheet: -1.79 (0.39), residues: 166 loop : -1.31 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.018 0.002 TYR A 372 PHE 0.012 0.001 PHE B 333 TRP 0.031 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8021) covalent geometry : angle 0.61057 (10795) hydrogen bonds : bond 0.03565 ( 316) hydrogen bonds : angle 6.35066 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 34 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8757 (ppp) cc_final: 0.8302 (ppp) REVERT: B 24 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9056 (mt) REVERT: B 125 MET cc_start: 0.6307 (pmm) cc_final: 0.5802 (pmm) REVERT: B 128 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: B 156 MET cc_start: 0.4598 (tpp) cc_final: 0.4343 (mmm) REVERT: B 300 TYR cc_start: 0.1537 (OUTLIER) cc_final: 0.1286 (m-10) REVERT: B 362 MET cc_start: 0.5294 (tpt) cc_final: 0.4896 (mmt) REVERT: B 421 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8999 (p0) REVERT: B 512 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.5388 (ppp) outliers start: 37 outliers final: 22 residues processed: 66 average time/residue: 0.0670 time to fit residues: 6.6118 Evaluate side-chains 59 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 32 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 81 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 0.0980 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 128 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.041474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.033711 restraints weight = 98264.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.034468 restraints weight = 71274.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.034991 restraints weight = 56487.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.035372 restraints weight = 47566.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.035653 restraints weight = 41845.609| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8021 Z= 0.183 Angle : 0.657 11.557 10795 Z= 0.338 Chirality : 0.042 0.161 1175 Planarity : 0.004 0.047 1374 Dihedral : 9.932 88.537 1110 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.06 % Allowed : 18.79 % Favored : 77.15 % 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 aren not related in a simple way. whole: -1.42 (0.27), residues: 947 helix: 0.22 (0.30), residues: 320 sheet: -1.88 (0.39), residues: 166 loop : -1.37 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 177 TYR 0.016 0.002 TYR A 372 PHE 0.017 0.001 PHE B 333 TRP 0.032 0.003 TRP A 311 HIS 0.008 0.002 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8021) covalent geometry : angle 0.65678 (10795) hydrogen bonds : bond 0.03800 ( 316) hydrogen bonds : angle 6.42857 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 31 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8696 (ppp) cc_final: 0.8403 (ppp) REVERT: B 125 MET cc_start: 0.6474 (pmm) cc_final: 0.5993 (pmm) REVERT: B 128 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: B 156 MET cc_start: 0.4732 (tpp) cc_final: 0.4446 (mmm) REVERT: B 362 MET cc_start: 0.5278 (tpt) cc_final: 0.4415 (tpp) REVERT: B 421 ASP cc_start: 0.9249 (OUTLIER) cc_final: 0.9008 (p0) REVERT: B 512 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.4613 (ppp) outliers start: 35 outliers final: 26 residues processed: 63 average time/residue: 0.0941 time to fit residues: 8.3392 Evaluate side-chains 61 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 32 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 0.0010 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 128 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.041993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.034153 restraints weight = 97358.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.034934 restraints weight = 70432.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.035460 restraints weight = 55630.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.035851 restraints weight = 46898.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.036109 restraints weight = 41213.688| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8021 Z= 0.141 Angle : 0.629 12.084 10795 Z= 0.325 Chirality : 0.042 0.149 1175 Planarity : 0.003 0.043 1374 Dihedral : 9.726 88.868 1110 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.71 % Allowed : 19.72 % Favored : 76.57 % 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 aren not related in a simple way. whole: -1.36 (0.27), residues: 947 helix: 0.27 (0.30), residues: 323 sheet: -1.83 (0.39), residues: 164 loop : -1.34 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.018 0.002 TYR A 372 PHE 0.020 0.001 PHE B 17 TRP 0.037 0.003 TRP A 311 HIS 0.007 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8021) covalent geometry : angle 0.62936 (10795) hydrogen bonds : bond 0.03650 ( 316) hydrogen bonds : angle 6.30246 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 32 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8693 (ppp) cc_final: 0.8332 (ppp) REVERT: B 125 MET cc_start: 0.6536 (pmm) cc_final: 0.6060 (pmm) REVERT: B 128 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: B 156 MET cc_start: 0.4682 (tpp) cc_final: 0.4413 (mmm) REVERT: B 362 MET cc_start: 0.5289 (tpt) cc_final: 0.4957 (mmt) REVERT: B 421 ASP cc_start: 0.9227 (OUTLIER) cc_final: 0.8984 (p0) REVERT: B 512 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5574 (ppp) outliers start: 32 outliers final: 26 residues processed: 61 average time/residue: 0.0878 time to fit residues: 7.7260 Evaluate side-chains 60 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 31 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 150 ASN Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 149 HIS ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.043070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.035172 restraints weight = 96189.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.035951 restraints weight = 69877.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.036503 restraints weight = 55368.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.036896 restraints weight = 46722.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.037172 restraints weight = 40985.634| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8021 Z= 0.114 Angle : 0.612 12.040 10795 Z= 0.315 Chirality : 0.042 0.144 1175 Planarity : 0.003 0.035 1374 Dihedral : 9.337 89.180 1110 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.25 % Allowed : 20.30 % Favored : 76.45 % 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 aren not related in a simple way. whole: -1.24 (0.27), residues: 947 helix: 0.40 (0.30), residues: 321 sheet: -1.80 (0.40), residues: 165 loop : -1.27 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.020 0.001 TYR A 372 PHE 0.018 0.001 PHE B 333 TRP 0.038 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8021) covalent geometry : angle 0.61201 (10795) hydrogen bonds : bond 0.03371 ( 316) hydrogen bonds : angle 6.12170 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 32 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: -0.0154 (mtp) cc_final: -0.0639 (mtt) REVERT: A 156 MET cc_start: 0.8689 (ppp) cc_final: 0.8338 (ppp) REVERT: B 52 ASP cc_start: 0.8339 (m-30) cc_final: 0.7609 (p0) REVERT: B 125 MET cc_start: 0.6624 (pmm) cc_final: 0.5900 (pmm) REVERT: B 156 MET cc_start: 0.4584 (tpp) cc_final: 0.4329 (mmm) REVERT: B 421 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8818 (p0) REVERT: B 512 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.5373 (ppp) outliers start: 28 outliers final: 21 residues processed: 58 average time/residue: 0.0853 time to fit residues: 7.2075 Evaluate side-chains 55 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 32 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 434 LYS Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 525 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.043033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.035001 restraints weight = 95662.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.035801 restraints weight = 69063.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.036364 restraints weight = 54556.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.036769 restraints weight = 45726.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.037036 restraints weight = 40150.396| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8021 Z= 0.119 Angle : 0.613 12.354 10795 Z= 0.315 Chirality : 0.042 0.141 1175 Planarity : 0.003 0.035 1374 Dihedral : 9.343 89.202 1110 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.55 % Allowed : 21.23 % Favored : 76.22 % 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 aren not related in a simple way. whole: -1.17 (0.28), residues: 947 helix: 0.42 (0.30), residues: 324 sheet: -1.84 (0.39), residues: 167 loop : -1.17 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 348 TYR 0.018 0.001 TYR A 372 PHE 0.017 0.001 PHE B 17 TRP 0.035 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8021) covalent geometry : angle 0.61330 (10795) hydrogen bonds : bond 0.03315 ( 316) hydrogen bonds : angle 6.03367 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1894 Ramachandran restraints generated. 947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 32 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: -0.0106 (mtp) cc_final: -0.0560 (mtt) REVERT: A 156 MET cc_start: 0.8702 (ppp) cc_final: 0.8425 (ppp) REVERT: B 52 ASP cc_start: 0.8369 (m-30) cc_final: 0.7593 (p0) REVERT: B 125 MET cc_start: 0.6676 (pmm) cc_final: 0.6019 (pmm) REVERT: B 156 MET cc_start: 0.4576 (tpp) cc_final: 0.4340 (mmm) REVERT: B 421 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8780 (p0) REVERT: B 512 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.5192 (ppp) outliers start: 22 outliers final: 16 residues processed: 53 average time/residue: 0.0872 time to fit residues: 6.6884 Evaluate side-chains 48 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 512 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 72 optimal weight: 30.0000 chunk 3 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 46 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.042192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.034376 restraints weight = 97211.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.035128 restraints weight = 70544.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.035655 restraints weight = 56063.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.036047 restraints weight = 47383.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.036332 restraints weight = 41634.677| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8021 Z= 0.155 Angle : 0.648 12.099 10795 Z= 0.335 Chirality : 0.042 0.149 1175 Planarity : 0.004 0.045 1374 Dihedral : 9.564 88.369 1110 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.32 % Allowed : 21.46 % Favored : 76.22 % 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 aren not related in a simple way. whole: -1.13 (0.27), residues: 947 helix: 0.43 (0.30), residues: 323 sheet: -1.80 (0.41), residues: 150 loop : -1.18 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.016 0.002 TYR A 372 PHE 0.017 0.001 PHE B 17 TRP 0.033 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8021) covalent geometry : angle 0.64796 (10795) hydrogen bonds : bond 0.03512 ( 316) hydrogen bonds : angle 6.08779 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.86 seconds wall clock time: 32 minutes 19.06 seconds (1939.06 seconds total)