Starting phenix.real_space_refine on Thu Jun 5 13:43:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyj_26181/06_2025/7tyj_26181_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyj_26181/06_2025/7tyj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyj_26181/06_2025/7tyj_26181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyj_26181/06_2025/7tyj_26181.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyj_26181/06_2025/7tyj_26181_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyj_26181/06_2025/7tyj_26181_neut.cif" } resolution = 3.3 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= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.18, per 1000 atoms: 0.66 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: 1.48 Conformation dependent library (CDL) restraints added in 920.0 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: 0.76 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: 1.88 Time building geometry restraints manager: 1.80 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.820 ------------------------------------------------------------------------------- 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 (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: -1.90 (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 TRP 0.007 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 PHE 0.012 0.002 PHE B 687 TYR 0.015 0.001 TYR A 56 ARG 0.002 0.000 ARG B 605 Details of bonding type rmsd hydrogen bonds : bond 0.16209 ( 135) hydrogen bonds : angle 6.07331 ( 348) SS BOND : bond 0.00223 ( 15) SS BOND : angle 1.03930 ( 30) covalent geometry : bond 0.00394 ( 6487) covalent geometry : angle 0.61981 ( 8817) *********************** 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 : 0.766 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.2998 time to fit residues: 23.0966 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 : 0.826 ------------------------------------------------------------------------------- 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 67 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.139749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.104856 restraints weight = 8487.237| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.66 r_work: 0.3046 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6502 Z= 0.130 Angle : 0.578 9.836 8847 Z= 0.295 Chirality : 0.044 0.170 983 Planarity : 0.004 0.046 1145 Dihedral : 5.333 51.623 890 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.67 % Favored : 90.20 % Rotamer: Outliers : 2.47 % Allowed : 18.90 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.29), residues: 796 helix: 0.32 (0.70), residues: 56 sheet: -0.65 (0.38), residues: 199 loop : -1.76 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 599 HIS 0.004 0.001 HIS A 123 PHE 0.010 0.001 PHE B 687 TYR 0.012 0.001 TYR A 56 ARG 0.002 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 135) hydrogen bonds : angle 5.17881 ( 348) SS BOND : bond 0.00257 ( 15) SS BOND : angle 0.89127 ( 30) covalent geometry : bond 0.00314 ( 6487) covalent geometry : angle 0.57615 ( 8817) *********************** 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 81 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 1.043 Fit side-chains REVERT: A 17 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7867 (ttp-110) REVERT: B 766 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.5357 (m-70) outliers start: 17 outliers final: 7 residues processed: 75 average time/residue: 0.2736 time to fit residues: 28.5433 Evaluate side-chains 67 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.139465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.103934 restraints weight = 8601.742| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.73 r_work: 0.3048 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0717 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= 0.106 Angle : 0.561 9.752 8847 Z= 0.284 Chirality : 0.043 0.191 983 Planarity : 0.004 0.045 1145 Dihedral : 5.142 51.725 888 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.17 % Favored : 90.70 % Rotamer: Outliers : 3.49 % Allowed : 19.19 % Favored : 77.33 % 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: -1.88 (0.29), residues: 796 helix: 0.06 (0.73), residues: 56 sheet: -0.66 (0.38), residues: 199 loop : -1.72 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.003 0.000 HIS A 123 PHE 0.009 0.001 PHE B 683 TYR 0.009 0.001 TYR A 56 ARG 0.002 0.000 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.02825 ( 135) hydrogen bonds : angle 4.96451 ( 348) SS BOND : bond 0.00214 ( 15) SS BOND : angle 0.79109 ( 30) covalent geometry : bond 0.00253 ( 6487) covalent geometry : angle 0.56035 ( 8817) *********************** 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 84 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 1.111 Fit side-chains REVERT: A 17 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7895 (ttp-110) REVERT: A 194 MET cc_start: 0.8294 (mtp) cc_final: 0.7989 (mtp) REVERT: A 253 ARG cc_start: 0.8261 (tpp-160) cc_final: 0.7317 (tpp80) REVERT: B 766 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.5438 (m-70) outliers start: 24 outliers final: 11 residues processed: 77 average time/residue: 0.2381 time to fit residues: 25.4086 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 : 0.716 ------------------------------------------------------------------------------- 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 52 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.098781 restraints weight = 8789.301| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.68 r_work: 0.2908 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 6502 Z= 0.296 Angle : 0.698 9.004 8847 Z= 0.353 Chirality : 0.049 0.230 983 Planarity : 0.005 0.051 1145 Dihedral : 5.970 58.992 888 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.93 % Favored : 87.94 % 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 (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: -2.18 (0.29), residues: 796 helix: -0.44 (0.69), residues: 56 sheet: -0.98 (0.38), residues: 196 loop : -1.84 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 599 HIS 0.005 0.001 HIS B 762 PHE 0.015 0.002 PHE B 734 TYR 0.018 0.002 TYR B 630 ARG 0.003 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 135) hydrogen bonds : angle 5.24690 ( 348) SS BOND : bond 0.00468 ( 15) SS BOND : angle 1.41077 ( 30) covalent geometry : bond 0.00724 ( 6487) covalent geometry : angle 0.69419 ( 8817) *********************** 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: 26 poor density : 54 time to evaluate : 0.774 Fit side-chains REVERT: A 17 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7972 (ttp-110) REVERT: B 506 HIS cc_start: 0.4384 (t70) cc_final: 0.4126 (t70) REVERT: B 692 HIS cc_start: 0.8338 (t70) cc_final: 0.8005 (t70) REVERT: B 766 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.5248 (m-70) outliers start: 26 outliers final: 17 residues processed: 74 average time/residue: 0.2029 time to fit residues: 20.5328 Evaluate side-chains 70 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 524 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 0.3980 chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.139257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104208 restraints weight = 8617.306| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.68 r_work: 0.3042 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6502 Z= 0.108 Angle : 0.589 9.324 8847 Z= 0.296 Chirality : 0.044 0.224 983 Planarity : 0.004 0.048 1145 Dihedral : 5.326 51.392 888 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.29 % Favored : 91.58 % Rotamer: Outliers : 2.91 % Allowed : 20.78 % Favored : 76.31 % 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: -1.99 (0.29), residues: 796 helix: -0.22 (0.70), residues: 56 sheet: -0.75 (0.38), residues: 199 loop : -1.77 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.002 0.000 HIS A 123 PHE 0.011 0.001 PHE B 683 TYR 0.010 0.001 TYR A 56 ARG 0.002 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.02805 ( 135) hydrogen bonds : angle 5.01113 ( 348) SS BOND : bond 0.00250 ( 15) SS BOND : angle 0.79993 ( 30) covalent geometry : bond 0.00255 ( 6487) covalent geometry : angle 0.58857 ( 8817) *********************** 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 79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.790 Fit side-chains REVERT: A 17 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7913 (ttp-110) REVERT: A 253 ARG cc_start: 0.8318 (tpp80) cc_final: 0.7996 (tpp-160) REVERT: B 766 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.5681 (m-70) outliers start: 20 outliers final: 11 residues processed: 72 average time/residue: 0.1896 time to fit residues: 18.7290 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 : 0.710 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 0.0270 chunk 43 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.0370 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105895 restraints weight = 8533.177| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.67 r_work: 0.3069 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1040 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= 0.097 Angle : 0.564 9.004 8847 Z= 0.282 Chirality : 0.044 0.238 983 Planarity : 0.004 0.045 1145 Dihedral : 5.060 48.134 888 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.17 % Favored : 90.70 % Rotamer: Outliers : 3.05 % Allowed : 21.66 % 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 (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: -1.90 (0.29), residues: 796 helix: -0.08 (0.71), residues: 56 sheet: -0.72 (0.38), residues: 199 loop : -1.69 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.003 0.000 HIS A 123 PHE 0.012 0.001 PHE A 267 TYR 0.008 0.001 TYR A 56 ARG 0.002 0.000 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 135) hydrogen bonds : angle 4.82656 ( 348) SS BOND : bond 0.00327 ( 15) SS BOND : angle 0.75862 ( 30) covalent geometry : bond 0.00226 ( 6487) covalent geometry : angle 0.56276 ( 8817) *********************** 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 81 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.754 Fit side-chains REVERT: A 17 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7907 (ttp-110) REVERT: A 253 ARG cc_start: 0.8130 (tpp80) cc_final: 0.7779 (tpp-160) REVERT: B 766 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.5921 (m-70) outliers start: 21 outliers final: 13 residues processed: 76 average time/residue: 0.1974 time to fit residues: 20.1972 Evaluate side-chains 71 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 31 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 64 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.137769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102672 restraints weight = 8595.104| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.64 r_work: 0.2984 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6502 Z= 0.174 Angle : 0.619 9.449 8847 Z= 0.307 Chirality : 0.046 0.222 983 Planarity : 0.004 0.047 1145 Dihedral : 5.396 51.533 888 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.92 % Favored : 89.95 % Rotamer: Outliers : 3.78 % Allowed : 20.64 % Favored : 75.58 % 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: -1.97 (0.29), residues: 796 helix: -0.31 (0.70), residues: 56 sheet: -0.79 (0.38), residues: 199 loop : -1.72 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 599 HIS 0.004 0.001 HIS B 762 PHE 0.013 0.002 PHE B 687 TYR 0.012 0.001 TYR B 494 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 135) hydrogen bonds : angle 4.93417 ( 348) SS BOND : bond 0.00269 ( 15) SS BOND : angle 0.98468 ( 30) covalent geometry : bond 0.00425 ( 6487) covalent geometry : angle 0.61706 ( 8817) *********************** 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 83 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.677 Fit side-chains REVERT: A 17 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7924 (ttp-110) REVERT: A 253 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7823 (tpp80) REVERT: B 692 HIS cc_start: 0.8336 (t70) cc_final: 0.8077 (t70) REVERT: B 766 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.5735 (m-70) outliers start: 26 outliers final: 17 residues processed: 76 average time/residue: 0.1923 time to fit residues: 19.7003 Evaluate side-chains 71 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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 737 GLN 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 830 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 17 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.135908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100194 restraints weight = 8645.235| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.69 r_work: 0.2985 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6502 Z= 0.210 Angle : 0.641 8.592 8847 Z= 0.321 Chirality : 0.047 0.248 983 Planarity : 0.004 0.049 1145 Dihedral : 5.657 53.694 888 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.93 % Favored : 88.94 % Rotamer: Outliers : 3.20 % Allowed : 21.37 % 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 (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: -2.08 (0.29), residues: 796 helix: -0.46 (0.69), residues: 56 sheet: -0.89 (0.38), residues: 194 loop : -1.76 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 599 HIS 0.004 0.001 HIS B 762 PHE 0.013 0.002 PHE B 687 TYR 0.014 0.001 TYR B 630 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 135) hydrogen bonds : angle 5.02829 ( 348) SS BOND : bond 0.00315 ( 15) SS BOND : angle 1.09881 ( 30) covalent geometry : bond 0.00513 ( 6487) covalent geometry : angle 0.63858 ( 8817) *********************** 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 74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 1.068 Fit side-chains REVERT: A 17 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7933 (ttp-110) REVERT: B 692 HIS cc_start: 0.8362 (t70) cc_final: 0.8083 (t70) REVERT: B 766 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.5679 (m-70) outliers start: 22 outliers final: 17 residues processed: 67 average time/residue: 0.2667 time to fit residues: 26.5702 Evaluate side-chains 71 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 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 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 830 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 18 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.137495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.102275 restraints weight = 8640.997| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.66 r_work: 0.3002 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6502 Z= 0.160 Angle : 0.621 10.490 8847 Z= 0.310 Chirality : 0.046 0.237 983 Planarity : 0.004 0.049 1145 Dihedral : 5.545 52.105 888 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.18 % Favored : 89.70 % Rotamer: Outliers : 3.34 % Allowed : 21.37 % 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 (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: -2.08 (0.29), residues: 796 helix: -0.47 (0.69), residues: 56 sheet: -0.89 (0.38), residues: 194 loop : -1.76 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 599 HIS 0.003 0.001 HIS B 762 PHE 0.012 0.002 PHE A 267 TYR 0.012 0.001 TYR B 630 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 135) hydrogen bonds : angle 4.98870 ( 348) SS BOND : bond 0.00276 ( 15) SS BOND : angle 0.95916 ( 30) covalent geometry : bond 0.00389 ( 6487) covalent geometry : angle 0.61987 ( 8817) *********************** 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 76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.735 Fit side-chains REVERT: A 253 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7535 (tpp80) REVERT: B 692 HIS cc_start: 0.8326 (t70) cc_final: 0.8055 (t70) REVERT: B 766 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.5762 (m-70) outliers start: 23 outliers final: 20 residues processed: 69 average time/residue: 0.1967 time to fit residues: 18.2672 Evaluate side-chains 72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 737 GLN 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 830 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 39 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 78 optimal weight: 1.9990 chunk 52 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 = 0.3620 r_free = 0.3620 target = 0.138241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103028 restraints weight = 8675.804| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.67 r_work: 0.3013 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1095 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= 0.141 Angle : 0.600 8.815 8847 Z= 0.301 Chirality : 0.045 0.234 983 Planarity : 0.004 0.047 1145 Dihedral : 5.445 51.010 888 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.80 % Favored : 90.08 % Rotamer: Outliers : 3.34 % Allowed : 21.37 % 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 (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: -2.04 (0.29), residues: 796 helix: -0.42 (0.69), residues: 56 sheet: -0.83 (0.38), residues: 199 loop : -1.76 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.003 0.001 HIS A 123 PHE 0.014 0.001 PHE A 267 TYR 0.010 0.001 TYR B 494 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 135) hydrogen bonds : angle 4.90227 ( 348) SS BOND : bond 0.00251 ( 15) SS BOND : angle 0.90203 ( 30) covalent geometry : bond 0.00341 ( 6487) covalent geometry : angle 0.59910 ( 8817) ********************** 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 78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 1.630 Fit side-chains REVERT: A 253 ARG cc_start: 0.7942 (tpp80) cc_final: 0.7368 (tpp-160) REVERT: A 381 MET cc_start: 0.7433 (ttp) cc_final: 0.7197 (ttt) REVERT: B 692 HIS cc_start: 0.8337 (t70) cc_final: 0.8083 (t70) REVERT: B 766 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.5960 (m-70) outliers start: 23 outliers final: 21 residues processed: 71 average time/residue: 0.3149 time to fit residues: 31.2291 Evaluate side-chains 75 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 1.291 ------------------------------------------------------------------------------- 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 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 737 GLN 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 830 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 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 23 optimal weight: 0.0970 chunk 62 optimal weight: 0.1980 chunk 50 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.141568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106134 restraints weight = 8726.467| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.74 r_work: 0.3074 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6502 Z= 0.088 Angle : 0.575 10.893 8847 Z= 0.284 Chirality : 0.044 0.250 983 Planarity : 0.004 0.044 1145 Dihedral : 5.011 46.756 888 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.30 % Favored : 90.58 % Rotamer: Outliers : 2.47 % Allowed : 22.53 % 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 (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: -1.90 (0.29), residues: 796 helix: -0.18 (0.70), residues: 56 sheet: -0.67 (0.38), residues: 199 loop : -1.70 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 246 HIS 0.002 0.000 HIS A 270 PHE 0.014 0.001 PHE A 267 TYR 0.007 0.001 TYR B 494 ARG 0.004 0.000 ARG A 17 Details of bonding type rmsd hydrogen bonds : bond 0.02471 ( 135) hydrogen bonds : angle 4.71975 ( 348) SS BOND : bond 0.00220 ( 15) SS BOND : angle 0.67884 ( 30) covalent geometry : bond 0.00198 ( 6487) covalent geometry : angle 0.57412 ( 8817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3572.79 seconds wall clock time: 65 minutes 8.74 seconds (3908.74 seconds total)