Starting phenix.real_space_refine on Tue Feb 11 16:50:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyj_26181/02_2025/7tyj_26181_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyj_26181/02_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_26181/02_2025/7tyj_26181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyj_26181/02_2025/7tyj_26181.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyj_26181/02_2025/7tyj_26181_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyj_26181/02_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-5592/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: 3.92, per 1000 atoms: 0.62 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: 1.35 Conformation dependent library (CDL) restraints added in 855.5 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: 0.68 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: 1.83 Time building geometry restraints manager: 1.62 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.230 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.800 ------------------------------------------------------------------------------- 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 6487 Z= 0.269 Angle : 0.620 9.842 8817 Z= 0.317 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 *********************** 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 : 0.751 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.2142 time to fit residues: 16.2999 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 : 0.724 ------------------------------------------------------------------------------- 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: 5.9990 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 = 8487.088| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.66 r_work: 0.3045 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6487 Z= 0.217 Angle : 0.576 9.836 8817 Z= 0.295 Chirality : 0.044 0.170 983 Planarity : 0.004 0.046 1145 Dihedral : 5.333 51.622 890 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 *********************** 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 : 0.704 Fit side-chains REVERT: A 17 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7868 (ttp-110) REVERT: B 766 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.5358 (m-70) outliers start: 17 outliers final: 7 residues processed: 75 average time/residue: 0.1894 time to fit residues: 19.4524 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 : 0.679 ------------------------------------------------------------------------------- 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: 0.2980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.140401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.104840 restraints weight = 8610.453| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.75 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: 0.8076 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6487 Z= 0.166 Angle : 0.559 9.790 8817 Z= 0.283 Chirality : 0.043 0.198 983 Planarity : 0.004 0.045 1145 Dihedral : 5.124 51.795 888 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.30 % Favored : 90.58 % Rotamer: Outliers : 3.34 % Allowed : 19.33 % 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: -1.87 (0.30), residues: 796 helix: 0.06 (0.73), residues: 56 sheet: -0.65 (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 0.010 0.001 PHE B 683 TYR 0.009 0.001 TYR A 56 ARG 0.002 0.000 ARG A 79 *********************** 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 83 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.663 Fit side-chains REVERT: A 17 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7897 (ttp-110) REVERT: A 194 MET cc_start: 0.8296 (mtp) cc_final: 0.8066 (mtp) REVERT: A 253 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.7320 (tpp80) REVERT: B 766 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.5489 (m-70) outliers start: 23 outliers final: 11 residues processed: 76 average time/residue: 0.1874 time to fit residues: 19.0809 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 : 0.762 ------------------------------------------------------------------------------- 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: 0.9980 chunk 10 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.134998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099635 restraints weight = 8768.044| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.68 r_work: 0.2916 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.006 0.069 6487 Z= 0.438 Angle : 0.661 9.146 8817 Z= 0.335 Chirality : 0.048 0.222 983 Planarity : 0.005 0.049 1145 Dihedral : 5.794 57.727 888 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.31 % Favored : 88.57 % Rotamer: Outliers : 4.22 % Allowed : 19.48 % 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: -2.09 (0.29), residues: 796 helix: -0.31 (0.70), residues: 56 sheet: -0.94 (0.38), residues: 196 loop : -1.78 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 599 HIS 0.005 0.001 HIS B 762 PHE 0.015 0.002 PHE B 548 TYR 0.016 0.002 TYR B 630 ARG 0.003 0.000 ARG A 10 *********************** 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 83 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.810 Fit side-chains REVERT: A 17 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7987 (ttp-110) REVERT: B 692 HIS cc_start: 0.8377 (t70) cc_final: 0.8061 (t70) REVERT: B 766 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.5469 (m-70) outliers start: 29 outliers final: 18 residues processed: 76 average time/residue: 0.1842 time to fit residues: 19.2620 Evaluate side-chains 70 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 61 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.138755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.103654 restraints weight = 8606.638| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.69 r_work: 0.3055 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6487 Z= 0.172 Angle : 0.583 9.646 8817 Z= 0.291 Chirality : 0.044 0.227 983 Planarity : 0.004 0.046 1145 Dihedral : 5.269 50.988 888 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.54 % Favored : 91.33 % Rotamer: Outliers : 2.76 % Allowed : 21.22 % 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: -1.94 (0.29), residues: 796 helix: -0.18 (0.71), residues: 56 sheet: -0.71 (0.38), residues: 199 loop : -1.73 (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 323 PHE 0.011 0.001 PHE B 687 TYR 0.010 0.001 TYR A 56 ARG 0.002 0.000 ARG A 437 *********************** 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: 19 poor density : 60 time to evaluate : 0.772 Fit side-chains REVERT: A 17 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7906 (ttp-110) REVERT: A 253 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8025 (tpp-160) REVERT: B 766 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.5589 (m-70) outliers start: 19 outliers final: 12 residues processed: 72 average time/residue: 0.1858 time to fit residues: 18.3910 Evaluate side-chains 67 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 615 LEU 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: 0.0670 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.0020 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.0050 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.3942 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.141351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106560 restraints weight = 8530.167| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.67 r_work: 0.3079 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6487 Z= 0.142 Angle : 0.557 9.501 8817 Z= 0.279 Chirality : 0.043 0.242 983 Planarity : 0.004 0.044 1145 Dihedral : 5.018 47.660 888 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 3.05 % Allowed : 21.51 % 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: -1.86 (0.30), residues: 796 helix: -0.03 (0.72), residues: 56 sheet: -0.68 (0.38), residues: 199 loop : -1.68 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.003 0.000 HIS A 123 PHE 0.012 0.001 PHE B 683 TYR 0.011 0.001 TYR B 480 ARG 0.002 0.000 ARG A 439 *********************** 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 82 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.704 Fit side-chains REVERT: A 17 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7938 (ttp-110) REVERT: A 253 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7775 (tpp-160) REVERT: B 766 HIS cc_start: 0.7125 (OUTLIER) cc_final: 0.5585 (m-70) outliers start: 21 outliers final: 13 residues processed: 77 average time/residue: 0.1871 time to fit residues: 19.7984 Evaluate side-chains 73 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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: 6.9990 chunk 68 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.134892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.099165 restraints weight = 8664.775| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.69 r_work: 0.2969 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 6487 Z= 0.442 Angle : 0.673 9.134 8817 Z= 0.338 Chirality : 0.048 0.247 983 Planarity : 0.005 0.049 1145 Dihedral : 5.747 55.084 888 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.68 % Favored : 88.19 % 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: -2.10 (0.29), residues: 796 helix: -0.49 (0.69), residues: 56 sheet: -0.93 (0.38), residues: 194 loop : -1.76 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 599 HIS 0.005 0.001 HIS B 762 PHE 0.015 0.002 PHE B 687 TYR 0.017 0.002 TYR B 630 ARG 0.003 0.000 ARG A 114 *********************** 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 76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.748 Fit side-chains REVERT: A 17 ARG cc_start: 0.8192 (ttp-110) cc_final: 0.7929 (ttp-110) REVERT: A 441 ASN cc_start: 0.8431 (p0) cc_final: 0.8180 (p0) REVERT: B 692 HIS cc_start: 0.8337 (t70) cc_final: 0.8045 (t70) REVERT: B 766 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.5422 (m-70) outliers start: 26 outliers final: 17 residues processed: 69 average time/residue: 0.1772 time to fit residues: 17.0122 Evaluate side-chains 67 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 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 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 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 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: 6.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 47 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.138856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103238 restraints weight = 8605.452| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.72 r_work: 0.3046 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.003 0.028 6487 Z= 0.188 Angle : 0.579 9.269 8817 Z= 0.290 Chirality : 0.044 0.224 983 Planarity : 0.004 0.047 1145 Dihedral : 5.303 49.829 888 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.92 % Favored : 90.95 % Rotamer: Outliers : 3.05 % Allowed : 20.93 % 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: -1.96 (0.29), residues: 796 helix: -0.30 (0.70), residues: 56 sheet: -0.77 (0.38), residues: 199 loop : -1.71 (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 0.010 0.001 PHE A 267 TYR 0.010 0.001 TYR B 494 ARG 0.001 0.000 ARG A 79 *********************** 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 73 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.732 Fit side-chains REVERT: A 17 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7930 (ttp-110) REVERT: A 253 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7542 (tpp-160) REVERT: B 766 HIS cc_start: 0.7288 (OUTLIER) cc_final: 0.5773 (m-70) outliers start: 21 outliers final: 17 residues processed: 66 average time/residue: 0.1922 time to fit residues: 17.2705 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 : 0.688 ------------------------------------------------------------------------------- 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 289 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.098583 restraints weight = 8720.042| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.64 r_work: 0.2956 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 6487 Z= 0.533 Angle : 0.714 10.747 8817 Z= 0.359 Chirality : 0.050 0.241 983 Planarity : 0.005 0.049 1145 Dihedral : 6.010 56.918 888 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.56 % Favored : 87.31 % Rotamer: Outliers : 3.05 % Allowed : 20.93 % 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: -2.26 (0.29), residues: 796 helix: -0.72 (0.68), residues: 56 sheet: -1.08 (0.38), residues: 196 loop : -1.85 (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 0.016 0.002 PHE B 548 TYR 0.019 0.002 TYR B 630 ARG 0.003 0.000 ARG A 10 *********************** 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 73 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.717 Fit side-chains REVERT: B 506 HIS cc_start: 0.4461 (t70) cc_final: 0.4176 (t70) REVERT: B 692 HIS cc_start: 0.8360 (t70) cc_final: 0.8069 (t70) REVERT: B 766 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.5582 (m-70) outliers start: 21 outliers final: 15 residues processed: 68 average time/residue: 0.1781 time to fit residues: 16.8547 Evaluate side-chains 63 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- 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 = 0.137857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102395 restraints weight = 8679.208| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.70 r_work: 0.3014 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6487 Z= 0.213 Angle : 0.600 9.073 8817 Z= 0.303 Chirality : 0.045 0.263 983 Planarity : 0.004 0.051 1145 Dihedral : 5.557 51.966 888 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.05 % Favored : 90.83 % Rotamer: Outliers : 2.62 % Allowed : 21.66 % 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 (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: -2.10 (0.29), residues: 796 helix: -0.49 (0.69), residues: 56 sheet: -0.92 (0.38), residues: 194 loop : -1.77 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.003 0.001 HIS B 762 PHE 0.013 0.001 PHE A 267 TYR 0.010 0.001 TYR A 56 ARG 0.002 0.000 ARG A 114 ********************** 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 67 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.778 Fit side-chains REVERT: A 253 ARG cc_start: 0.7892 (tpp80) cc_final: 0.7550 (tpp80) REVERT: B 692 HIS cc_start: 0.8356 (t70) cc_final: 0.8088 (t70) REVERT: B 766 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.5893 (m-70) outliers start: 18 outliers final: 14 residues processed: 62 average time/residue: 0.1965 time to fit residues: 16.4132 Evaluate side-chains 64 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 67 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 50 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 overall best weight: 0.2876 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.141694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106176 restraints weight = 8741.339| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.75 r_work: 0.3096 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6487 Z= 0.137 Angle : 0.569 10.694 8817 Z= 0.283 Chirality : 0.044 0.243 983 Planarity : 0.004 0.044 1145 Dihedral : 5.011 46.949 888 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.92 % Favored : 89.95 % Rotamer: Outliers : 2.03 % Allowed : 22.24 % 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 (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: -1.91 (0.29), residues: 796 helix: -0.17 (0.70), residues: 56 sheet: -0.72 (0.38), residues: 199 loop : -1.70 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.003 0.000 HIS A 123 PHE 0.013 0.001 PHE B 683 TYR 0.007 0.001 TYR B 494 ARG 0.004 0.000 ARG A 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.51 seconds wall clock time: 52 minutes 55.29 seconds (3175.29 seconds total)