Starting phenix.real_space_refine on Tue Mar 11 16:22:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyj_26181/03_2025/7tyj_26181_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyj_26181/03_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_26181/03_2025/7tyj_26181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyj_26181/03_2025/7tyj_26181.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyj_26181/03_2025/7tyj_26181_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyj_26181/03_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-5624/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: 3.84, per 1000 atoms: 0.61 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: 1.31 Conformation dependent library (CDL) restraints added in 828.9 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: 0.77 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: 2.04 Time building geometry restraints manager: 1.61 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: 0.570 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.920 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- 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 : 0.729 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.2125 time to fit residues: 16.1719 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 : 0.725 ------------------------------------------------------------------------------- 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 = 8487.237| |-----------------------------------------------------------------------------| 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 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 51.623 890 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 *********************** 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 : 0.664 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: 0.1811 time to fit residues: 18.4210 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 : 0.714 ------------------------------------------------------------------------------- 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: 1.9990 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: 7.9990 chunk 59 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 = 0.3640 r_free = 0.3640 target = 0.139787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104183 restraints weight = 8615.641| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.75 r_work: 0.3055 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0698 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= 0.178 Angle : 0.562 9.759 8817 Z= 0.285 Chirality : 0.043 0.197 983 Planarity : 0.004 0.045 1145 Dihedral : 5.165 51.943 888 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.17 % Favored : 90.70 % Rotamer: Outliers : 3.49 % Allowed : 19.04 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.89 (0.29), residues: 796 helix: 0.05 (0.72), residues: 56 sheet: -0.66 (0.38), residues: 199 loop : -1.73 (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 0.010 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: 24 poor density : 59 time to evaluate : 0.677 Fit side-chains REVERT: A 17 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7896 (ttp-110) REVERT: A 194 MET cc_start: 0.8307 (mtp) cc_final: 0.8008 (mtp) REVERT: A 253 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7328 (tpp80) REVERT: B 766 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.5448 (m-70) outliers start: 24 outliers final: 11 residues processed: 76 average time/residue: 0.1846 time to fit residues: 18.9684 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 : 0.711 ------------------------------------------------------------------------------- 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: 4.9990 chunk 51 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 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: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.136014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100284 restraints weight = 8773.405| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.73 r_work: 0.2983 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6487 Z= 0.345 Angle : 0.620 9.329 8817 Z= 0.313 Chirality : 0.046 0.213 983 Planarity : 0.004 0.047 1145 Dihedral : 5.545 54.981 888 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.93 % Favored : 88.94 % Rotamer: Outliers : 3.63 % Allowed : 20.06 % 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: -2.02 (0.29), residues: 796 helix: -0.15 (0.71), residues: 56 sheet: -0.91 (0.38), residues: 188 loop : -1.73 (0.26), residues: 552 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 734 TYR 0.013 0.001 TYR B 494 ARG 0.002 0.000 ARG A 437 *********************** 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 79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.745 Fit side-chains REVERT: A 17 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7953 (ttp-110) REVERT: A 253 ARG cc_start: 0.8302 (tpp-160) cc_final: 0.7361 (tpp80) REVERT: B 692 HIS cc_start: 0.8322 (t70) cc_final: 0.8021 (t70) REVERT: B 766 HIS cc_start: 0.7248 (OUTLIER) cc_final: 0.5364 (m-70) outliers start: 25 outliers final: 14 residues processed: 72 average time/residue: 0.1781 time to fit residues: 17.6178 Evaluate side-chains 68 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103475 restraints weight = 8661.212| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.74 r_work: 0.3029 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0851 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= 0.183 Angle : 0.573 9.615 8817 Z= 0.288 Chirality : 0.044 0.220 983 Planarity : 0.004 0.046 1145 Dihedral : 5.234 51.475 888 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.67 % Favored : 91.21 % Rotamer: Outliers : 3.34 % Allowed : 20.49 % Favored : 76.16 % 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: -0.07 (0.71), residues: 56 sheet: -0.71 (0.38), residues: 199 loop : -1.71 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 123 PHE 0.010 0.001 PHE B 687 TYR 0.010 0.001 TYR A 56 ARG 0.002 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.677 Fit side-chains REVERT: A 17 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7943 (ttp-110) REVERT: A 253 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7302 (tpp80) REVERT: B 766 HIS cc_start: 0.7245 (OUTLIER) cc_final: 0.5591 (m-70) outliers start: 23 outliers final: 16 residues processed: 76 average time/residue: 0.1781 time to fit residues: 18.5254 Evaluate side-chains 70 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 283 THR Chi-restraints excluded: chain A residue 322 THR 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 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.138982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104006 restraints weight = 8545.367| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.67 r_work: 0.3003 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6487 Z= 0.214 Angle : 0.577 9.377 8817 Z= 0.290 Chirality : 0.044 0.225 983 Planarity : 0.004 0.044 1145 Dihedral : 5.238 50.878 888 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.55 % Favored : 90.33 % Rotamer: Outliers : 4.22 % Allowed : 20.20 % 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: -1.89 (0.29), residues: 796 helix: -0.04 (0.71), residues: 56 sheet: -0.74 (0.38), residues: 199 loop : -1.68 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 599 HIS 0.003 0.001 HIS A 123 PHE 0.011 0.001 PHE B 687 TYR 0.010 0.001 TYR B 494 ARG 0.002 0.000 ARG A 224 *********************** 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 85 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.673 Fit side-chains REVERT: A 17 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7904 (ttp-110) REVERT: A 253 ARG cc_start: 0.8213 (tpp-160) cc_final: 0.7304 (tpp80) REVERT: B 766 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.5648 (m-70) outliers start: 29 outliers final: 21 residues processed: 78 average time/residue: 0.1800 time to fit residues: 19.1825 Evaluate side-chains 79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 283 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 31 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.137996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102394 restraints weight = 8628.792| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.72 r_work: 0.3031 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6487 Z= 0.235 Angle : 0.588 9.241 8817 Z= 0.294 Chirality : 0.045 0.238 983 Planarity : 0.004 0.046 1145 Dihedral : 5.306 51.518 888 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.42 % Favored : 90.45 % Rotamer: Outliers : 4.22 % Allowed : 20.35 % 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: -1.92 (0.29), residues: 796 helix: -0.12 (0.70), residues: 56 sheet: -0.78 (0.37), residues: 199 loop : -1.68 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 599 HIS 0.003 0.001 HIS A 123 PHE 0.011 0.001 PHE B 687 TYR 0.011 0.001 TYR B 494 ARG 0.001 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 87 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.660 Fit side-chains REVERT: A 17 ARG cc_start: 0.8174 (ttp-110) cc_final: 0.7915 (ttp-110) REVERT: A 253 ARG cc_start: 0.8146 (tpp-160) cc_final: 0.7302 (tpp80) REVERT: B 692 HIS cc_start: 0.8328 (t70) cc_final: 0.8067 (t70) REVERT: B 766 HIS cc_start: 0.7211 (OUTLIER) cc_final: 0.5449 (m-70) outliers start: 29 outliers final: 23 residues processed: 80 average time/residue: 0.1712 time to fit residues: 18.8968 Evaluate side-chains 78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 489 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 879 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.139281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.103661 restraints weight = 8601.902| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.72 r_work: 0.3050 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1007 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= 0.188 Angle : 0.572 9.411 8817 Z= 0.286 Chirality : 0.044 0.214 983 Planarity : 0.004 0.044 1145 Dihedral : 5.190 49.665 888 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.55 % Favored : 90.33 % 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: -1.87 (0.29), residues: 796 helix: -0.07 (0.70), residues: 56 sheet: -0.74 (0.38), residues: 199 loop : -1.65 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.003 0.001 HIS A 123 PHE 0.010 0.001 PHE B 683 TYR 0.009 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 82 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.696 Fit side-chains REVERT: A 17 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7916 (ttp-110) REVERT: A 253 ARG cc_start: 0.8177 (tpp-160) cc_final: 0.7286 (tpp80) REVERT: B 766 HIS cc_start: 0.7255 (OUTLIER) cc_final: 0.5606 (m-70) outliers start: 26 outliers final: 20 residues processed: 75 average time/residue: 0.1819 time to fit residues: 18.8912 Evaluate side-chains 76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 270 HIS Chi-restraints excluded: chain A residue 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 489 LEU Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 766 HIS Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 879 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.135086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099472 restraints weight = 8713.382| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.70 r_work: 0.2982 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6487 Z= 0.408 Angle : 0.668 9.786 8817 Z= 0.334 Chirality : 0.048 0.249 983 Planarity : 0.004 0.048 1145 Dihedral : 5.724 55.085 888 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.93 % Favored : 87.94 % Rotamer: Outliers : 3.63 % Allowed : 20.78 % 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: -2.06 (0.29), residues: 796 helix: -0.34 (0.69), residues: 56 sheet: -0.92 (0.38), residues: 194 loop : -1.74 (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 0.014 0.002 PHE B 687 TYR 0.016 0.002 TYR B 630 ARG 0.002 0.000 ARG A 247 *********************** 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 77 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.765 Fit side-chains REVERT: A 17 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7928 (ttp-110) REVERT: B 692 HIS cc_start: 0.8343 (t70) cc_final: 0.8059 (t70) REVERT: B 766 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.5427 (m-70) outliers start: 25 outliers final: 20 residues processed: 70 average time/residue: 0.1925 time to fit residues: 18.6533 Evaluate side-chains 70 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 489 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.137972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102250 restraints weight = 8707.119| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.73 r_work: 0.3030 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6487 Z= 0.218 Angle : 0.601 9.104 8817 Z= 0.302 Chirality : 0.045 0.237 983 Planarity : 0.004 0.048 1145 Dihedral : 5.414 51.288 888 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.85 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: -1.99 (0.29), residues: 796 helix: -0.32 (0.69), residues: 56 sheet: -0.87 (0.38), residues: 194 loop : -1.69 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 B 494 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 77 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.713 Fit side-chains REVERT: A 17 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7928 (ttp-110) REVERT: A 253 ARG cc_start: 0.8437 (tpp80) cc_final: 0.7606 (tpp80) REVERT: B 692 HIS cc_start: 0.8337 (t70) cc_final: 0.8083 (t70) REVERT: B 766 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.5696 (m-70) outliers start: 21 outliers final: 18 residues processed: 70 average time/residue: 0.1976 time to fit residues: 18.5421 Evaluate side-chains 73 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 322 THR Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 489 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 0.0020 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.140662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105236 restraints weight = 8742.727| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.74 r_work: 0.3074 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6487 Z= 0.150 Angle : 0.579 9.908 8817 Z= 0.288 Chirality : 0.044 0.235 983 Planarity : 0.004 0.043 1145 Dihedral : 5.035 47.896 888 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.05 % Favored : 90.83 % Rotamer: Outliers : 2.62 % Allowed : 21.95 % 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 (0.29), residues: 796 helix: -0.18 (0.70), residues: 56 sheet: -0.71 (0.38), residues: 199 loop : -1.64 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 246 HIS 0.003 0.001 HIS A 123 PHE 0.012 0.001 PHE B 683 TYR 0.008 0.001 TYR B 494 ARG 0.004 0.000 ARG A 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.51 seconds wall clock time: 52 minutes 41.00 seconds (3161.00 seconds total)