Starting phenix.real_space_refine on Tue Mar 3 14:48:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyj_26181/03_2026/7tyj_26181_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyj_26181/03_2026/7tyj_26181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tyj_26181/03_2026/7tyj_26181_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyj_26181/03_2026/7tyj_26181_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyj_26181/03_2026/7tyj_26181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyj_26181/03_2026/7tyj_26181.map" } resolution = 3.3 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 4008 2.51 5 N 1129 2.21 5 O 1162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6338 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3437 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 21, 'TRANS': 425} Chain breaks: 1 Chain: "B" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2901 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 23, 'TRANS': 337} Chain breaks: 3 Time building chain proxies: 1.47, per 1000 atoms: 0.23 Number of scatterers: 6338 At special positions: 0 Unit cell: (81, 85.32, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1162 8.00 N 1129 7.00 C 4008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 223 " - pdb=" SG CYS A 232 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 838 " distance=2.03 Simple disulfide: pdb=" SG CYS B 764 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 334.1 milliseconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1502 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 15 sheets defined 11.8% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.671A pdb=" N GLN A 18 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 19 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.938A pdb=" N LEU A 131 " --> pdb=" O ASP A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.556A pdb=" N GLY A 272 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.717A pdb=" N HIS A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.805A pdb=" N ILE A 427 " --> pdb=" O CYS A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 626 Processing helix chain 'B' and resid 678 through 693 removed outlier: 3.661A pdb=" N LEU B 691 " --> pdb=" O PHE B 687 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN B 693 " --> pdb=" O ASN B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 848 removed outlier: 4.128A pdb=" N PHE B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 removed outlier: 8.359A pdb=" N GLN A 30 " --> pdb=" O PRO A 5 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 7 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N LEU A 32 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A 9 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET A 34 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 62 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 57 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE A 92 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A 59 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR A 87 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG A 114 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 89 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU A 116 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 91 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.733A pdb=" N THR A 168 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 175 " --> pdb=" O THR A 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283 removed outlier: 3.574A pdb=" N HIS A 292 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 309 removed outlier: 6.573A pdb=" N HIS A 323 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS A 303 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 325 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY A 305 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 327 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 309 removed outlier: 6.573A pdb=" N HIS A 323 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS A 303 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 325 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLY A 305 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 327 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR A 415 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR A 389 " --> pdb=" O TYR A 415 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA A 417 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 391 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 459 through 460 removed outlier: 5.958A pdb=" N ARG B 459 " --> pdb=" O GLN B 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 463 through 468 removed outlier: 3.584A pdb=" N SER B 465 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 521 through 523 Processing sheet with id=AB3, first strand: chain 'B' and resid 583 through 591 removed outlier: 5.821A pdb=" N ASP B 584 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS B 600 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN B 590 " --> pdb=" O HIS B 594 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N HIS B 594 " --> pdb=" O ASN B 590 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 737 through 741 removed outlier: 3.782A pdb=" N GLN B 737 " --> pdb=" O TRP B 616 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP B 616 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 611 " --> pdb=" O CYS B 764 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 756 " --> pdb=" O LEU B 619 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 797 through 798 Processing sheet with id=AB6, first strand: chain 'B' and resid 835 through 840 138 hydrogen bonds defined for protein. 348 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: 0.96 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2119 1.34 - 1.46: 1485 1.46 - 1.58: 2839 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 6487 Sorted by residual: bond pdb=" CA THR A 436 " pdb=" CB THR A 436 " ideal model delta sigma weight residual 1.527 1.554 -0.027 2.48e-02 1.63e+03 1.15e+00 bond pdb=" CB LYS A 359 " pdb=" CG LYS A 359 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.95e-01 bond pdb=" CB ASP A 317 " pdb=" CG ASP A 317 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.93e-01 bond pdb=" N THR B 553 " pdb=" CA THR B 553 " ideal model delta sigma weight residual 1.460 1.471 -0.012 1.42e-02 4.96e+03 6.56e-01 bond pdb=" CG1 ILE A 127 " pdb=" CD1 ILE A 127 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 6.00e-01 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 8663 1.97 - 3.94: 129 3.94 - 5.91: 19 5.91 - 7.87: 3 7.87 - 9.84: 3 Bond angle restraints: 8817 Sorted by residual: angle pdb=" CA LEU B 627 " pdb=" CB LEU B 627 " pdb=" CG LEU B 627 " ideal model delta sigma weight residual 116.30 126.14 -9.84 3.50e+00 8.16e-02 7.91e+00 angle pdb=" CB MET A 381 " pdb=" CG MET A 381 " pdb=" SD MET A 381 " ideal model delta sigma weight residual 112.70 104.36 8.34 3.00e+00 1.11e-01 7.73e+00 angle pdb=" CG1 ILE A 269 " pdb=" CB ILE A 269 " pdb=" CG2 ILE A 269 " ideal model delta sigma weight residual 110.70 102.76 7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" C THR A 54 " pdb=" N ASP A 55 " pdb=" CA ASP A 55 " ideal model delta sigma weight residual 122.42 118.58 3.84 1.55e+00 4.16e-01 6.12e+00 angle pdb=" C TRP A 246 " pdb=" N ARG A 247 " pdb=" CA ARG A 247 " ideal model delta sigma weight residual 122.36 118.56 3.80 1.60e+00 3.91e-01 5.63e+00 ... (remaining 8812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 3365 18.02 - 36.05: 417 36.05 - 54.07: 100 54.07 - 72.09: 18 72.09 - 90.12: 11 Dihedral angle restraints: 3911 sinusoidal: 1580 harmonic: 2331 Sorted by residual: dihedral pdb=" CB CYS A 190 " pdb=" SG CYS A 190 " pdb=" SG CYS A 202 " pdb=" CB CYS A 202 " ideal model delta sinusoidal sigma weight residual 93.00 -176.88 -90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS A 165 " pdb=" SG CYS A 165 " pdb=" SG CYS A 184 " pdb=" CB CYS A 184 " ideal model delta sinusoidal sigma weight residual -86.00 -161.16 75.16 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CA ARG A 10 " pdb=" C ARG A 10 " pdb=" N SER A 11 " pdb=" CA SER A 11 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 3908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 709 0.042 - 0.085: 181 0.085 - 0.127: 86 0.127 - 0.170: 5 0.170 - 0.212: 2 Chirality restraints: 983 Sorted by residual: chirality pdb=" CB ILE A 269 " pdb=" CA ILE A 269 " pdb=" CG1 ILE A 269 " pdb=" CG2 ILE A 269 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU A 226 " pdb=" CB LEU A 226 " pdb=" CD1 LEU A 226 " pdb=" CD2 LEU A 226 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TRP A 246 " pdb=" N TRP A 246 " pdb=" C TRP A 246 " pdb=" CB TRP A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 980 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 697 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 698 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 698 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 698 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 190 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 191 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 445 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C ILE A 445 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE A 445 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 446 " -0.011 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 242 2.71 - 3.26: 5971 3.26 - 3.80: 9459 3.80 - 4.35: 12108 4.35 - 4.90: 21165 Nonbonded interactions: 48945 Sorted by model distance: nonbonded pdb=" OG SER B 801 " pdb=" OG SER B 805 " model vdw 2.161 3.040 nonbonded pdb=" O HIS B 766 " pdb=" OG1 THR B 770 " model vdw 2.171 3.040 nonbonded pdb=" O PRO B 856 " pdb=" OH TYR B 860 " model vdw 2.206 3.040 nonbonded pdb=" O LEU A 430 " pdb=" OG1 THR A 434 " model vdw 2.225 3.040 nonbonded pdb=" O ALA A 315 " pdb=" OG SER A 345 " model vdw 2.247 3.040 ... (remaining 48940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6502 Z= 0.164 Angle : 0.622 9.842 8847 Z= 0.318 Chirality : 0.046 0.212 983 Planarity : 0.004 0.056 1145 Dihedral : 16.632 86.456 2364 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.30 % Favored : 89.57 % Rotamer: Outliers : 0.44 % Allowed : 21.08 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.29), residues: 796 helix: 0.26 (0.70), residues: 56 sheet: -0.59 (0.38), residues: 201 loop : -1.81 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 605 TYR 0.015 0.001 TYR A 56 PHE 0.012 0.002 PHE B 687 TRP 0.007 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6487) covalent geometry : angle 0.61981 ( 8817) SS BOND : bond 0.00223 ( 15) SS BOND : angle 1.03930 ( 30) hydrogen bonds : bond 0.16209 ( 135) hydrogen bonds : angle 6.07331 ( 348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.245 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.0943 time to fit residues: 7.1853 Evaluate side-chains 58 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 488 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102254 restraints weight = 8596.814| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.70 r_work: 0.3019 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6502 Z= 0.172 Angle : 0.604 9.759 8847 Z= 0.309 Chirality : 0.045 0.170 983 Planarity : 0.005 0.048 1145 Dihedral : 5.512 53.561 890 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer: Outliers : 2.62 % Allowed : 19.19 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.29), residues: 796 helix: -0.10 (0.72), residues: 56 sheet: -0.70 (0.38), residues: 199 loop : -1.81 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.013 0.001 TYR A 56 PHE 0.011 0.002 PHE B 687 TRP 0.009 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6487) covalent geometry : angle 0.60211 ( 8817) SS BOND : bond 0.00281 ( 15) SS BOND : angle 1.00702 ( 30) hydrogen bonds : bond 0.03661 ( 135) hydrogen bonds : angle 5.24059 ( 348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.250 Fit side-chains REVERT: A 17 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7839 (ttp-110) REVERT: B 766 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.5390 (m-70) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 0.0924 time to fit residues: 8.9186 Evaluate side-chains 68 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 766 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 0.0020 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102846 restraints weight = 8611.322| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.73 r_work: 0.3019 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6502 Z= 0.126 Angle : 0.577 9.714 8847 Z= 0.293 Chirality : 0.044 0.188 983 Planarity : 0.004 0.047 1145 Dihedral : 5.319 53.218 888 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 3.34 % Allowed : 19.19 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.29), residues: 796 helix: -0.06 (0.72), residues: 56 sheet: -0.71 (0.38), residues: 199 loop : -1.76 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 224 TYR 0.010 0.001 TYR A 56 PHE 0.010 0.001 PHE B 687 TRP 0.008 0.001 TRP A 246 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6487) covalent geometry : angle 0.57580 ( 8817) SS BOND : bond 0.00239 ( 15) SS BOND : angle 0.87354 ( 30) hydrogen bonds : bond 0.03046 ( 135) hydrogen bonds : angle 5.07181 ( 348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.254 Fit side-chains REVERT: A 17 ARG cc_start: 0.8205 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: A 194 MET cc_start: 0.8310 (mtp) cc_final: 0.8014 (mtp) REVERT: A 253 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7322 (tpp80) REVERT: B 766 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.5532 (m-70) outliers start: 23 outliers final: 11 residues processed: 75 average time/residue: 0.0851 time to fit residues: 8.6215 Evaluate side-chains 67 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 766 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105062 restraints weight = 8629.913| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.67 r_work: 0.3044 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6502 Z= 0.116 Angle : 0.568 9.623 8847 Z= 0.286 Chirality : 0.044 0.221 983 Planarity : 0.004 0.045 1145 Dihedral : 5.205 50.558 888 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 3.20 % Allowed : 20.35 % 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 are not related in a simple way. whole: -1.90 (0.29), residues: 796 helix: -0.00 (0.72), residues: 56 sheet: -0.69 (0.38), residues: 199 loop : -1.72 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.009 0.001 TYR A 56 PHE 0.010 0.001 PHE B 687 TRP 0.008 0.001 TRP A 246 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6487) covalent geometry : angle 0.56706 ( 8817) SS BOND : bond 0.00234 ( 15) SS BOND : angle 0.82690 ( 30) hydrogen bonds : bond 0.02847 ( 135) hydrogen bonds : angle 4.95276 ( 348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.257 Fit side-chains REVERT: A 17 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7966 (ttp-110) REVERT: A 253 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.7323 (tpp80) REVERT: B 766 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.5422 (m-70) outliers start: 22 outliers final: 13 residues processed: 73 average time/residue: 0.0816 time to fit residues: 8.0356 Evaluate side-chains 69 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101702 restraints weight = 8758.077| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.74 r_work: 0.3008 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6502 Z= 0.163 Angle : 0.599 9.369 8847 Z= 0.301 Chirality : 0.045 0.221 983 Planarity : 0.004 0.047 1145 Dihedral : 5.399 53.007 888 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.80 % Favored : 90.08 % Rotamer: Outliers : 3.78 % Allowed : 20.20 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.29), residues: 796 helix: -0.11 (0.70), residues: 56 sheet: -0.76 (0.38), residues: 199 loop : -1.74 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.012 0.001 TYR B 494 PHE 0.011 0.001 PHE B 687 TRP 0.009 0.001 TRP B 599 HIS 0.004 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6487) covalent geometry : angle 0.59709 ( 8817) SS BOND : bond 0.00268 ( 15) SS BOND : angle 0.98343 ( 30) hydrogen bonds : bond 0.03091 ( 135) hydrogen bonds : angle 4.98661 ( 348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.228 Fit side-chains REVERT: A 17 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7920 (ttp-110) REVERT: A 253 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7323 (tpp80) REVERT: B 766 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.5478 (m-70) outliers start: 26 outliers final: 19 residues processed: 76 average time/residue: 0.0757 time to fit residues: 7.8634 Evaluate side-chains 78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 737 GLN Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 737 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.103702 restraints weight = 8696.757| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.67 r_work: 0.2974 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6502 Z= 0.126 Angle : 0.578 9.420 8847 Z= 0.291 Chirality : 0.044 0.227 983 Planarity : 0.004 0.046 1145 Dihedral : 5.312 51.364 888 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 4.07 % Allowed : 20.20 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.29), residues: 796 helix: -0.08 (0.71), residues: 56 sheet: -0.76 (0.38), residues: 199 loop : -1.71 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.010 0.001 TYR B 494 PHE 0.012 0.001 PHE A 267 TRP 0.009 0.001 TRP A 246 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6487) covalent geometry : angle 0.57698 ( 8817) SS BOND : bond 0.00230 ( 15) SS BOND : angle 0.84951 ( 30) hydrogen bonds : bond 0.02877 ( 135) hydrogen bonds : angle 4.93473 ( 348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.208 Fit side-chains REVERT: A 17 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7877 (ttp-110) REVERT: A 253 ARG cc_start: 0.8197 (tpp-160) cc_final: 0.7283 (tpp80) REVERT: B 766 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.5598 (m-70) outliers start: 28 outliers final: 22 residues processed: 81 average time/residue: 0.0696 time to fit residues: 7.7605 Evaluate side-chains 80 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102683 restraints weight = 8611.973| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.67 r_work: 0.3024 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6502 Z= 0.156 Angle : 0.604 9.222 8847 Z= 0.301 Chirality : 0.045 0.231 983 Planarity : 0.004 0.046 1145 Dihedral : 5.398 52.341 888 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.30 % Favored : 89.57 % Rotamer: Outliers : 4.51 % Allowed : 20.06 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.29), residues: 796 helix: -0.15 (0.70), residues: 56 sheet: -0.82 (0.37), residues: 199 loop : -1.72 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.011 0.001 TYR B 494 PHE 0.012 0.002 PHE A 267 TRP 0.009 0.001 TRP B 599 HIS 0.004 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6487) covalent geometry : angle 0.60290 ( 8817) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.94796 ( 30) hydrogen bonds : bond 0.03030 ( 135) hydrogen bonds : angle 4.94556 ( 348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.245 Fit side-chains REVERT: A 17 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: A 253 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7304 (tpp80) REVERT: B 692 HIS cc_start: 0.8329 (t70) cc_final: 0.8060 (t70) REVERT: B 766 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.5428 (m-70) outliers start: 31 outliers final: 22 residues processed: 82 average time/residue: 0.0711 time to fit residues: 8.0319 Evaluate side-chains 78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.0770 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105395 restraints weight = 8661.022| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.70 r_work: 0.3064 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6502 Z= 0.099 Angle : 0.568 9.535 8847 Z= 0.285 Chirality : 0.044 0.216 983 Planarity : 0.004 0.044 1145 Dihedral : 5.140 48.387 888 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.05 % Favored : 90.83 % Rotamer: Outliers : 3.34 % Allowed : 21.22 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.29), residues: 796 helix: -0.07 (0.70), residues: 56 sheet: -0.75 (0.38), residues: 199 loop : -1.68 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.009 0.001 TYR A 56 PHE 0.012 0.001 PHE A 267 TRP 0.010 0.001 TRP A 246 HIS 0.002 0.000 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6487) covalent geometry : angle 0.56760 ( 8817) SS BOND : bond 0.00201 ( 15) SS BOND : angle 0.69699 ( 30) hydrogen bonds : bond 0.02667 ( 135) hydrogen bonds : angle 4.85598 ( 348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.229 Fit side-chains REVERT: A 17 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7918 (ttp-110) REVERT: A 253 ARG cc_start: 0.8153 (tpp-160) cc_final: 0.7271 (tpp80) REVERT: B 766 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.5548 (m-70) REVERT: B 827 TYR cc_start: 0.8671 (p90) cc_final: 0.8112 (p90) outliers start: 23 outliers final: 16 residues processed: 78 average time/residue: 0.0794 time to fit residues: 8.3133 Evaluate side-chains 75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103595 restraints weight = 8721.919| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.74 r_work: 0.3052 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6502 Z= 0.120 Angle : 0.586 9.450 8847 Z= 0.293 Chirality : 0.044 0.232 983 Planarity : 0.004 0.044 1145 Dihedral : 5.176 48.657 888 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 2.91 % Allowed : 21.80 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.29), residues: 796 helix: -0.07 (0.70), residues: 56 sheet: -0.76 (0.38), residues: 199 loop : -1.67 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.009 0.001 TYR B 494 PHE 0.013 0.001 PHE A 267 TRP 0.008 0.001 TRP A 246 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6487) covalent geometry : angle 0.58543 ( 8817) SS BOND : bond 0.00224 ( 15) SS BOND : angle 0.79109 ( 30) hydrogen bonds : bond 0.02792 ( 135) hydrogen bonds : angle 4.87000 ( 348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.236 Fit side-chains REVERT: A 17 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7932 (ttp-110) REVERT: A 253 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.7263 (tpp80) REVERT: B 766 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.5709 (m-70) outliers start: 20 outliers final: 18 residues processed: 72 average time/residue: 0.0785 time to fit residues: 7.6905 Evaluate side-chains 76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102793 restraints weight = 8586.877| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.71 r_work: 0.3021 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6502 Z= 0.142 Angle : 0.597 9.200 8847 Z= 0.299 Chirality : 0.045 0.272 983 Planarity : 0.004 0.045 1145 Dihedral : 5.306 50.241 888 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer: Outliers : 3.05 % Allowed : 21.95 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.29), residues: 796 helix: -0.11 (0.70), residues: 56 sheet: -0.77 (0.38), residues: 199 loop : -1.67 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.025 0.001 TYR B 860 PHE 0.014 0.001 PHE A 267 TRP 0.009 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6487) covalent geometry : angle 0.59565 ( 8817) SS BOND : bond 0.00251 ( 15) SS BOND : angle 0.84985 ( 30) hydrogen bonds : bond 0.02929 ( 135) hydrogen bonds : angle 4.88483 ( 348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.260 Fit side-chains REVERT: A 17 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7931 (ttp-110) REVERT: A 253 ARG cc_start: 0.8053 (tpp-160) cc_final: 0.7255 (tpp80) REVERT: B 692 HIS cc_start: 0.8330 (t70) cc_final: 0.8080 (t70) REVERT: B 766 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.5546 (m-70) outliers start: 21 outliers final: 18 residues processed: 71 average time/residue: 0.0732 time to fit residues: 7.1048 Evaluate side-chains 74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 0.0470 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104013 restraints weight = 8720.636| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.73 r_work: 0.3028 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6502 Z= 0.107 Angle : 0.585 9.769 8847 Z= 0.291 Chirality : 0.044 0.253 983 Planarity : 0.004 0.044 1145 Dihedral : 5.141 48.788 888 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.80 % Favored : 90.08 % Rotamer: Outliers : 2.62 % Allowed : 22.24 % Favored : 75.15 % 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 are not related in a simple way. whole: -1.85 (0.29), residues: 796 helix: -0.04 (0.70), residues: 56 sheet: -0.73 (0.38), residues: 199 loop : -1.65 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 437 TYR 0.015 0.001 TYR B 860 PHE 0.012 0.001 PHE A 267 TRP 0.010 0.001 TRP A 246 HIS 0.003 0.001 HIS B 762 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6487) covalent geometry : angle 0.58410 ( 8817) SS BOND : bond 0.00226 ( 15) SS BOND : angle 0.74042 ( 30) hydrogen bonds : bond 0.02705 ( 135) hydrogen bonds : angle 4.81920 ( 348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.85 seconds wall clock time: 24 minutes 5.02 seconds (1445.02 seconds total)