Starting phenix.real_space_refine on Wed Feb 12 12:45:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u1m_41817/02_2025/8u1m_41817.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u1m_41817/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u1m_41817/02_2025/8u1m_41817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u1m_41817/02_2025/8u1m_41817.map" model { file = "/net/cci-nas-00/data/ceres_data/8u1m_41817/02_2025/8u1m_41817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u1m_41817/02_2025/8u1m_41817.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.04, per 1000 atoms: 0.64 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 2.25 Time building geometry restraints manager: 2.32 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: 0.980 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.520 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.170 ------------------------------------------------------------------------------- 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= 0.405 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (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 TRP 0.046 0.003 TRP A 311 HIS 0.007 0.001 HIS A 314 PHE 0.010 0.001 PHE A 208 TYR 0.015 0.002 TYR A 372 ARG 0.006 0.000 ARG A 177 *********************** 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 : 1.092 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: 0.2386 time to fit residues: 12.4121 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 : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 435 ASN A 446 ASN 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 406 ASN B 431 GLN ** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.041613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.033877 restraints weight = 95703.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.034582 restraints weight = 69573.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.035109 restraints weight = 55499.721| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8021 Z= 0.315 Angle : 0.691 7.831 10795 Z= 0.371 Chirality : 0.044 0.163 1175 Planarity : 0.004 0.046 1374 Dihedral : 10.541 88.615 1110 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 23.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.67 % Allowed : 18.56 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.27), residues: 947 helix: -0.00 (0.29), residues: 320 sheet: -1.52 (0.40), residues: 162 loop : -1.36 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 311 HIS 0.009 0.002 HIS A 314 PHE 0.012 0.002 PHE A 84 TYR 0.017 0.002 TYR B 519 ARG 0.006 0.001 ARG A 177 *********************** 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 54 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 31 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8752 (ppp) cc_final: 0.8445 (ppp) REVERT: B 84 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7151 (t80) outliers start: 23 outliers final: 11 residues processed: 52 average time/residue: 0.1786 time to fit residues: 14.0353 Evaluate side-chains 43 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 84 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 147 SER 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 94 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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** B 118 GLN ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** 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 = 0.3928 r_free = 0.3928 target = 0.041957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.034184 restraints weight = 97722.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.034958 restraints weight = 70309.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.035510 restraints weight = 55408.365| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8021 Z= 0.243 Angle : 0.614 7.211 10795 Z= 0.331 Chirality : 0.043 0.155 1175 Planarity : 0.004 0.050 1374 Dihedral : 10.151 83.845 1110 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.06 % Allowed : 17.17 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.27), residues: 947 helix: 0.05 (0.29), residues: 320 sheet: -1.67 (0.40), residues: 161 loop : -1.33 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 311 HIS 0.008 0.002 HIS A 314 PHE 0.009 0.001 PHE B 303 TYR 0.015 0.002 TYR A 372 ARG 0.005 0.001 ARG A 177 *********************** 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 68 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 33 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8740 (ppp) cc_final: 0.8475 (ppp) REVERT: B 421 ASP cc_start: 0.9263 (OUTLIER) cc_final: 0.9035 (p0) outliers start: 35 outliers final: 18 residues processed: 66 average time/residue: 0.1667 time to fit residues: 16.5669 Evaluate side-chains 53 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 271 ILE Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 30 ASN 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 275 TYR 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 Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 507 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 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 = 0.3943 r_free = 0.3943 target = 0.042356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.034550 restraints weight = 94743.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.035312 restraints weight = 68639.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.035847 restraints weight = 54378.636| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8021 Z= 0.200 Angle : 0.607 9.100 10795 Z= 0.321 Chirality : 0.042 0.153 1175 Planarity : 0.003 0.046 1374 Dihedral : 9.952 84.142 1110 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.36 % Allowed : 18.33 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.27), residues: 947 helix: 0.22 (0.30), residues: 320 sheet: -1.75 (0.40), residues: 163 loop : -1.23 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.016 0.001 PHE B 165 TYR 0.017 0.002 TYR A 372 ARG 0.004 0.000 ARG A 177 *********************** 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 64 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 35 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8755 (ppp) cc_final: 0.8333 (ppp) REVERT: B 421 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.9041 (p0) REVERT: B 512 MET cc_start: 0.5366 (ppp) cc_final: 0.5025 (ppp) outliers start: 29 outliers final: 17 residues processed: 62 average time/residue: 0.1774 time to fit residues: 16.1667 Evaluate side-chains 52 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR 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 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 507 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 88 optimal weight: 0.3980 chunk 89 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 overall best weight: 2.8984 ------------------------------------------------------------------------------- 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 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 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 = 0.042197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.034361 restraints weight = 95345.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.035127 restraints weight = 69037.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.035651 restraints weight = 54882.729| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8021 Z= 0.205 Angle : 0.612 15.600 10795 Z= 0.318 Chirality : 0.042 0.141 1175 Planarity : 0.003 0.046 1374 Dihedral : 9.857 84.774 1110 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.94 % Allowed : 18.56 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 947 helix: 0.24 (0.30), residues: 323 sheet: -1.80 (0.39), residues: 168 loop : -1.29 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.015 0.001 PHE B 17 TYR 0.016 0.002 TYR A 372 ARG 0.004 0.000 ARG A 177 *********************** 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 68 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 34 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.0727 (mtp) cc_final: 0.0495 (mtp) REVERT: A 156 MET cc_start: 0.8710 (ppp) cc_final: 0.8420 (ppp) REVERT: B 421 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.9052 (p0) REVERT: B 512 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.5111 (ppp) outliers start: 34 outliers final: 24 residues processed: 64 average time/residue: 0.2057 time to fit residues: 18.6969 Evaluate side-chains 58 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 32 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 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 A residue 453 LEU 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 151 ASP Chi-restraints excluded: chain B residue 275 TYR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 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 = 0.3923 r_free = 0.3923 target = 0.041968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.034148 restraints weight = 96183.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.034905 restraints weight = 69954.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.035426 restraints weight = 55592.221| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8021 Z= 0.214 Angle : 0.616 10.307 10795 Z= 0.321 Chirality : 0.042 0.141 1175 Planarity : 0.003 0.043 1374 Dihedral : 9.740 85.819 1110 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.29 % Allowed : 18.79 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 947 helix: 0.28 (0.30), residues: 323 sheet: -1.84 (0.39), residues: 168 loop : -1.29 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 311 HIS 0.007 0.001 HIS A 314 PHE 0.012 0.001 PHE B 17 TYR 0.016 0.002 TYR A 372 ARG 0.005 0.000 ARG A 391 *********************** 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 : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.0723 (mtp) cc_final: 0.0224 (mtt) REVERT: A 156 MET cc_start: 0.8730 (ppp) cc_final: 0.8478 (ppp) REVERT: B 128 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.6737 (tm-30) REVERT: B 362 MET cc_start: 0.5338 (tpt) cc_final: 0.4545 (tpp) REVERT: B 421 ASP cc_start: 0.9286 (OUTLIER) cc_final: 0.9045 (p0) REVERT: B 512 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.5347 (ppp) outliers start: 37 outliers final: 24 residues processed: 67 average time/residue: 0.2065 time to fit residues: 19.4381 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 : 0.901 ------------------------------------------------------------------------------- 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 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 A residue 453 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 overall best weight: 2.9784 ------------------------------------------------------------------------------- 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 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 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 = 0.3918 r_free = 0.3918 target = 0.041904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.034097 restraints weight = 95468.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.034846 restraints weight = 69010.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.035380 restraints weight = 54768.587| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8021 Z= 0.207 Angle : 0.621 13.894 10795 Z= 0.322 Chirality : 0.042 0.141 1175 Planarity : 0.003 0.045 1374 Dihedral : 9.705 85.760 1110 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.48 % Allowed : 20.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.27), residues: 947 helix: 0.31 (0.30), residues: 320 sheet: -1.85 (0.39), residues: 166 loop : -1.27 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.010 0.001 PHE B 17 TYR 0.018 0.002 TYR B 300 ARG 0.004 0.000 ARG A 391 *********************** 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 63 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 33 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8728 (ppp) cc_final: 0.8456 (ppp) REVERT: B 125 MET cc_start: 0.6401 (pmm) cc_final: 0.5897 (pmm) REVERT: B 362 MET cc_start: 0.5323 (tpt) cc_final: 0.4526 (tpp) REVERT: B 421 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.9096 (p0) REVERT: B 475 MET cc_start: 0.4641 (mtt) cc_final: 0.4331 (ptp) REVERT: B 512 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.5282 (ppp) outliers start: 30 outliers final: 26 residues processed: 60 average time/residue: 0.2007 time to fit residues: 17.4040 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 : 0.984 ------------------------------------------------------------------------------- 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 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 A residue 453 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 135 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 128 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 GLN ** 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 = 0.3870 r_free = 0.3870 target = 0.040504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.032852 restraints weight = 98537.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.033595 restraints weight = 71090.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.034109 restraints weight = 56218.185| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8021 Z= 0.313 Angle : 0.709 13.018 10795 Z= 0.368 Chirality : 0.043 0.144 1175 Planarity : 0.004 0.057 1374 Dihedral : 10.094 88.855 1110 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 25.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.18 % Allowed : 19.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 947 helix: 0.08 (0.29), residues: 318 sheet: -2.08 (0.40), residues: 159 loop : -1.29 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 311 HIS 0.007 0.002 HIS A 314 PHE 0.023 0.002 PHE B 17 TYR 0.024 0.002 TYR A 275 ARG 0.006 0.001 ARG A 177 *********************** 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 67 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 31 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.0235 (mtp) cc_final: -0.0003 (mtm) REVERT: B 362 MET cc_start: 0.5321 (tpt) cc_final: 0.4363 (tpp) REVERT: B 421 ASP cc_start: 0.9225 (OUTLIER) cc_final: 0.8944 (p0) REVERT: B 512 MET cc_start: 0.5819 (OUTLIER) cc_final: 0.5606 (ppp) outliers start: 36 outliers final: 29 residues processed: 64 average time/residue: 0.1941 time to fit residues: 17.9564 Evaluate side-chains 62 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 31 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 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 A residue 453 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 135 SER 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 65 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 74 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 374 ASN ** 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 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.041722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.033920 restraints weight = 97955.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.034714 restraints weight = 69817.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.035264 restraints weight = 54713.373| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8021 Z= 0.201 Angle : 0.641 11.397 10795 Z= 0.330 Chirality : 0.042 0.143 1175 Planarity : 0.003 0.044 1374 Dihedral : 9.644 88.600 1110 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.48 % Allowed : 21.11 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.27), residues: 947 helix: 0.24 (0.30), residues: 320 sheet: -1.95 (0.40), residues: 163 loop : -1.31 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 311 HIS 0.005 0.001 HIS A 314 PHE 0.019 0.001 PHE B 17 TYR 0.018 0.002 TYR A 372 ARG 0.004 0.000 ARG A 177 *********************** 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 62 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 32 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 125 MET cc_start: 0.6386 (pmm) cc_final: 0.5846 (pmm) REVERT: B 362 MET cc_start: 0.5294 (tpt) cc_final: 0.5066 (mmt) REVERT: B 421 ASP cc_start: 0.9304 (OUTLIER) cc_final: 0.9050 (p0) REVERT: B 512 MET cc_start: 0.5580 (OUTLIER) cc_final: 0.5333 (ppp) outliers start: 30 outliers final: 24 residues processed: 59 average time/residue: 0.1960 time to fit residues: 16.9035 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 : 1.043 ------------------------------------------------------------------------------- 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 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 135 SER 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 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 51 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 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 = 0.3857 r_free = 0.3857 target = 0.040176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.032630 restraints weight = 99698.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.033364 restraints weight = 71621.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.033875 restraints weight = 56464.552| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8021 Z= 0.352 Angle : 0.749 11.401 10795 Z= 0.388 Chirality : 0.044 0.145 1175 Planarity : 0.004 0.056 1374 Dihedral : 10.110 89.813 1110 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 27.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.36 % Allowed : 20.88 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.27), residues: 947 helix: 0.02 (0.29), residues: 318 sheet: -1.97 (0.40), residues: 157 loop : -1.30 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP A 311 HIS 0.007 0.002 HIS A 314 PHE 0.011 0.002 PHE A 84 TYR 0.022 0.002 TYR A 275 ARG 0.006 0.001 ARG A 177 ********************** 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 60 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 31 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 125 MET cc_start: 0.6361 (pmm) cc_final: 0.5874 (pmm) REVERT: B 362 MET cc_start: 0.5270 (tpt) cc_final: 0.4299 (tpp) REVERT: B 421 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.9027 (p0) REVERT: B 512 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5738 (ppp) outliers start: 29 outliers final: 26 residues processed: 57 average time/residue: 0.2064 time to fit residues: 17.1474 Evaluate side-chains 59 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 31 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 135 SER 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 518 GLU 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 93 optimal weight: 0.2980 chunk 86 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 44 optimal weight: 0.0970 chunk 11 optimal weight: 5.9990 overall best weight: 3.8784 ------------------------------------------------------------------------------- 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 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 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 = 0.3883 r_free = 0.3883 target = 0.040986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.033370 restraints weight = 98257.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.034140 restraints weight = 70213.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.034656 restraints weight = 55075.767| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8021 Z= 0.253 Angle : 0.681 10.919 10795 Z= 0.351 Chirality : 0.043 0.150 1175 Planarity : 0.004 0.049 1374 Dihedral : 9.828 88.819 1110 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.48 % Allowed : 20.88 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.27), residues: 947 helix: 0.01 (0.29), residues: 323 sheet: -1.94 (0.41), residues: 149 loop : -1.34 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 311 HIS 0.006 0.001 HIS A 314 PHE 0.011 0.001 PHE A 129 TYR 0.019 0.002 TYR B 300 ARG 0.007 0.001 ARG A 391 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.89 seconds wall clock time: 55 minutes 12.60 seconds (3312.60 seconds total)