Starting phenix.real_space_refine on Thu Jul 2 02:34:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7to1_26026/07_2026/7to1_26026.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to1_26026/07_2026/7to1_26026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2026/7to1_26026.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2026/7to1_26026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2026/7to1_26026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2026/7to1_26026.map" model { file = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2026/7to1_26026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2026/7to1_26026.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 24 5.49 5 S 31 5.16 5 C 3492 2.51 5 N 947 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5601 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 477 Unusual residues: {'GTP': 1} Classifications: {'RNA': 21, 'undetermined': 1} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4191 SG CYS A 810 43.045 22.013 23.953 1.00 50.21 S ATOM 4630 SG CYS A 864 42.729 20.263 20.098 1.00 64.66 S ATOM 4669 SG CYS A 869 39.685 21.192 21.887 1.00 60.38 S Time building chain proxies: 1.36, per 1000 atoms: 0.24 Number of scatterers: 5601 At special positions: 0 Unit cell: (89.25, 94.5, 66.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 24 15.00 O 1106 8.00 N 947 7.00 C 3492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 181.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 50.2% alpha, 8.7% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.711A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.725A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.534A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.068A pdb=" N GLN A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 492 through 497 removed outlier: 4.366A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 removed outlier: 3.674A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.698A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.598A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.960A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 650 removed outlier: 3.714A pdb=" N VAL A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 771 removed outlier: 4.107A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 794 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.561A pdb=" N LYS A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 840' Processing helix chain 'A' and resid 889 through 892 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 removed outlier: 7.202A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 461 through 462 removed outlier: 3.744A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 712 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU A 741 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 714 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 3.857A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.405A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846 removed outlier: 5.729A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 895 1.32 - 1.44: 1579 1.44 - 1.57: 3195 1.57 - 1.69: 46 1.69 - 1.82: 43 Bond restraints: 5758 Sorted by residual: bond pdb=" C1' GTP B 1 " pdb=" C2' GTP B 1 " ideal model delta sigma weight residual 1.524 1.285 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1' GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C5 GTP B 1 " pdb=" C6 GTP B 1 " ideal model delta sigma weight residual 1.390 1.544 -0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" C4 GTP B 1 " pdb=" N3 GTP B 1 " ideal model delta sigma weight residual 1.355 1.490 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6868 1.63 - 3.27: 981 3.27 - 4.90: 18 4.90 - 6.54: 2 6.54 - 8.17: 3 Bond angle restraints: 7872 Sorted by residual: angle pdb=" CA GLY A 835 " pdb=" C GLY A 835 " pdb=" O GLY A 835 " ideal model delta sigma weight residual 121.41 118.49 2.92 8.80e-01 1.29e+00 1.10e+01 angle pdb=" C VAL A 453 " pdb=" N TYR A 454 " pdb=" CA TYR A 454 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CA VAL A 414 " pdb=" C VAL A 414 " pdb=" O VAL A 414 " ideal model delta sigma weight residual 120.34 117.52 2.82 9.10e-01 1.21e+00 9.62e+00 angle pdb=" N ILE A 489 " pdb=" CA ILE A 489 " pdb=" C ILE A 489 " ideal model delta sigma weight residual 113.53 110.85 2.68 9.80e-01 1.04e+00 7.50e+00 angle pdb=" C2' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" C4' GTP B 1 " ideal model delta sigma weight residual 111.00 102.83 8.17 3.00e+00 1.11e-01 7.42e+00 ... (remaining 7867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.24: 3212 20.24 - 40.47: 215 40.47 - 60.70: 22 60.70 - 80.93: 10 80.93 - 101.17: 2 Dihedral angle restraints: 3461 sinusoidal: 1589 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 3.43 101.17 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" C4' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " ideal model delta sinusoidal sigma weight residual -99.13 -165.63 66.50 1 2.00e+01 2.50e-03 1.44e+01 dihedral pdb=" CA LEU A 449 " pdb=" C LEU A 449 " pdb=" N GLU A 450 " pdb=" CA GLU A 450 " ideal model delta harmonic sigma weight residual -180.00 -161.31 -18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 411 0.041 - 0.081: 265 0.081 - 0.122: 188 0.122 - 0.162: 27 0.162 - 0.203: 2 Chirality restraints: 893 Sorted by residual: chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE A 261 " pdb=" N ILE A 261 " pdb=" C ILE A 261 " pdb=" CB ILE A 261 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA ILE A 386 " pdb=" N ILE A 386 " pdb=" C ILE A 386 " pdb=" CB ILE A 386 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 890 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 62 " 0.028 2.00e-02 2.50e+03 1.31e-02 3.86e+00 pdb=" N1 U B 62 " -0.011 2.00e-02 2.50e+03 pdb=" C2 U B 62 " -0.010 2.00e-02 2.50e+03 pdb=" O2 U B 62 " -0.008 2.00e-02 2.50e+03 pdb=" N3 U B 62 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 62 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 62 " 0.014 2.00e-02 2.50e+03 pdb=" C5 U B 62 " -0.008 2.00e-02 2.50e+03 pdb=" C6 U B 62 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 697 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C THR A 697 " 0.021 2.00e-02 2.50e+03 pdb=" O THR A 697 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 698 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 60 " 0.017 2.00e-02 2.50e+03 6.79e-03 1.38e+00 pdb=" N9 G B 60 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G B 60 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 60 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 60 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 60 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 60 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 60 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G B 60 " -0.004 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1634 2.83 - 3.35: 5465 3.35 - 3.87: 9347 3.87 - 4.38: 10237 4.38 - 4.90: 17565 Nonbonded interactions: 44248 Sorted by model distance: nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.314 3.040 nonbonded pdb=" OH TYR A 622 " pdb=" OD1 ASN A 692 " model vdw 2.315 3.040 nonbonded pdb=" NH1 ARG A 811 " pdb=" O GLU A 890 " model vdw 2.336 3.120 nonbonded pdb=" O ILE A 337 " pdb=" ND2 ASN A 341 " model vdw 2.339 3.120 nonbonded pdb=" OG SER A 362 " pdb=" OG SER A 364 " model vdw 2.364 3.040 ... (remaining 44243 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.830 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.015 0.676 5762 Z= 0.890 Angle : 1.047 8.173 7872 Z= 0.756 Chirality : 0.063 0.203 893 Planarity : 0.004 0.019 924 Dihedral : 13.191 101.166 2241 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.31), residues: 627 helix: 0.24 (0.29), residues: 282 sheet: -3.75 (0.50), residues: 67 loop : -2.85 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 316 TYR 0.015 0.003 TYR A 390 PHE 0.016 0.003 PHE A 460 TRP 0.010 0.003 TRP A 873 HIS 0.005 0.002 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.01213 / 0.83 ( 5758) covalent geometry : angle 1.04703 / 0.76 ( 7872) hydrogen bonds : bond 0.13076 / 8.55 ( 260) hydrogen bonds : angle 5.07344 / 3.51 ( 737) metal coordination : bond 0.40819 / 21.35 ( 3) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8601 (mptt) REVERT: A 287 GLN cc_start: 0.8710 (tp40) cc_final: 0.8243 (pm20) REVERT: A 298 ASN cc_start: 0.8022 (t0) cc_final: 0.7806 (t0) REVERT: A 373 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 388 PHE cc_start: 0.8300 (m-10) cc_final: 0.7722 (m-80) REVERT: A 481 ASP cc_start: 0.7314 (m-30) cc_final: 0.7111 (m-30) REVERT: A 525 MET cc_start: 0.7566 (mmt) cc_final: 0.7181 (mmp) REVERT: A 531 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8079 (tt0) REVERT: A 556 GLU cc_start: 0.7822 (tt0) cc_final: 0.7565 (mt-10) REVERT: A 598 GLU cc_start: 0.8597 (tp30) cc_final: 0.8378 (tp30) REVERT: A 603 ASP cc_start: 0.8437 (t0) cc_final: 0.7931 (t70) REVERT: A 773 GLU cc_start: 0.7947 (tt0) cc_final: 0.7544 (tm-30) REVERT: A 803 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8739 (mmmt) REVERT: A 907 LYS cc_start: 0.8642 (mttt) cc_final: 0.8119 (mtmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0997 time to fit residues: 16.3287 Evaluate side-chains 87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 GLN A 495 ASN A 517 GLN A 557 HIS A 595 GLN A 769 GLN A 784 GLN A 876 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.139611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113563 restraints weight = 6908.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117119 restraints weight = 4338.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119749 restraints weight = 3165.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121471 restraints weight = 2524.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122849 restraints weight = 2153.669| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5762 Z= 0.116 Angle : 0.533 8.071 7872 Z= 0.266 Chirality : 0.039 0.238 893 Planarity : 0.003 0.040 924 Dihedral : 6.816 88.862 935 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.93 % Allowed : 12.08 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.34), residues: 627 helix: 1.30 (0.31), residues: 292 sheet: -3.30 (0.54), residues: 74 loop : -2.60 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 602 TYR 0.013 0.001 TYR A 622 PHE 0.008 0.001 PHE A 295 TRP 0.007 0.001 TRP A 771 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 5758) covalent geometry : angle 0.53346 / 0.27 ( 7872) hydrogen bonds : bond 0.03775 / 2.47 ( 260) hydrogen bonds : angle 3.73202 / 2.55 ( 737) metal coordination : bond 0.00681 / 0.34 ( 3) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8241 (mtt) cc_final: 0.7989 (mtt) REVERT: A 298 ASN cc_start: 0.8051 (t0) cc_final: 0.7828 (t0) REVERT: A 511 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 529 ASP cc_start: 0.8065 (t0) cc_final: 0.7841 (t0) REVERT: A 541 TYR cc_start: 0.8146 (m-80) cc_final: 0.7891 (m-80) REVERT: A 556 GLU cc_start: 0.7375 (tt0) cc_final: 0.7156 (mt-10) REVERT: A 596 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8162 (tm-30) REVERT: A 598 GLU cc_start: 0.8062 (tp30) cc_final: 0.7760 (tp30) REVERT: A 907 LYS cc_start: 0.8589 (mttt) cc_final: 0.8068 (mtmm) outliers start: 11 outliers final: 5 residues processed: 98 average time/residue: 0.0798 time to fit residues: 10.2789 Evaluate side-chains 80 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 890 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 0.0770 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN A 608 ASN A 619 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121773 restraints weight = 6669.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.124302 restraints weight = 4907.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125459 restraints weight = 4247.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126177 restraints weight = 3173.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.126374 restraints weight = 3017.098| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5762 Z= 0.143 Angle : 0.547 7.685 7872 Z= 0.274 Chirality : 0.039 0.179 893 Planarity : 0.003 0.036 924 Dihedral : 6.864 89.588 935 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.63 % Allowed : 16.29 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.34), residues: 627 helix: 1.55 (0.31), residues: 293 sheet: -3.29 (0.57), residues: 68 loop : -2.49 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 602 TYR 0.012 0.002 TYR A 622 PHE 0.011 0.001 PHE A 295 TRP 0.004 0.001 TRP A 771 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5758) covalent geometry : angle 0.54724 / 0.27 ( 7872) hydrogen bonds : bond 0.03974 / 2.61 ( 260) hydrogen bonds : angle 3.75803 / 2.58 ( 737) metal coordination : bond 0.00332 / 0.17 ( 3) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 GLU cc_start: 0.7869 (tp30) cc_final: 0.7656 (tp30) REVERT: A 283 LYS cc_start: 0.8839 (tppt) cc_final: 0.8372 (mmtt) REVERT: A 298 ASN cc_start: 0.8103 (t0) cc_final: 0.7848 (t0) REVERT: A 511 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 529 ASP cc_start: 0.8011 (t0) cc_final: 0.7729 (t0) REVERT: A 541 TYR cc_start: 0.8068 (m-80) cc_final: 0.7790 (m-80) REVERT: A 907 LYS cc_start: 0.8587 (mttt) cc_final: 0.8241 (mtmm) outliers start: 15 outliers final: 11 residues processed: 94 average time/residue: 0.0812 time to fit residues: 9.9768 Evaluate side-chains 84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130314 restraints weight = 6458.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133483 restraints weight = 4704.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134649 restraints weight = 3835.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135226 restraints weight = 2921.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135454 restraints weight = 2792.236| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5762 Z= 0.141 Angle : 0.543 7.620 7872 Z= 0.274 Chirality : 0.039 0.153 893 Planarity : 0.004 0.045 924 Dihedral : 6.815 89.140 935 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.68 % Allowed : 16.81 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.35), residues: 627 helix: 1.71 (0.31), residues: 293 sheet: -3.15 (0.60), residues: 68 loop : -2.35 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 602 TYR 0.013 0.001 TYR A 622 PHE 0.010 0.001 PHE A 295 TRP 0.005 0.001 TRP A 512 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 5758) covalent geometry : angle 0.54278 / 0.27 ( 7872) hydrogen bonds : bond 0.03878 / 2.55 ( 260) hydrogen bonds : angle 3.69309 / 2.54 ( 737) metal coordination : bond 0.00264 / 0.14 ( 3) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8839 (tppt) cc_final: 0.8512 (mmtt) REVERT: A 298 ASN cc_start: 0.8108 (t0) cc_final: 0.7822 (t0) REVERT: A 511 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7667 (tm-30) REVERT: A 529 ASP cc_start: 0.7987 (t0) cc_final: 0.7698 (t0) REVERT: A 541 TYR cc_start: 0.8061 (m-80) cc_final: 0.7782 (m-80) REVERT: A 879 TYR cc_start: 0.7725 (t80) cc_final: 0.7506 (t80) REVERT: A 907 LYS cc_start: 0.8617 (mttt) cc_final: 0.8274 (mtmm) outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 0.0714 time to fit residues: 8.8923 Evaluate side-chains 87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 890 GLU Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129809 restraints weight = 6538.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132585 restraints weight = 4525.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133947 restraints weight = 4039.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134586 restraints weight = 3003.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135166 restraints weight = 2762.853| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5762 Z= 0.117 Angle : 0.527 7.410 7872 Z= 0.266 Chirality : 0.038 0.141 893 Planarity : 0.003 0.036 924 Dihedral : 6.700 88.911 935 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.98 % Allowed : 18.21 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.35), residues: 627 helix: 1.85 (0.31), residues: 293 sheet: -2.94 (0.63), residues: 66 loop : -2.26 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.013 0.001 TYR A 622 PHE 0.009 0.001 PHE A 295 TRP 0.009 0.001 TRP A 646 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 5758) covalent geometry : angle 0.52702 / 0.27 ( 7872) hydrogen bonds : bond 0.03702 / 2.42 ( 260) hydrogen bonds : angle 3.64761 / 2.53 ( 737) metal coordination : bond 0.00205 / 0.11 ( 3) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8902 (tppt) cc_final: 0.8560 (mptt) REVERT: A 298 ASN cc_start: 0.8141 (t0) cc_final: 0.7833 (t0) REVERT: A 511 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 529 ASP cc_start: 0.8067 (t0) cc_final: 0.7713 (t0) REVERT: A 541 TYR cc_start: 0.8045 (m-10) cc_final: 0.7829 (m-80) REVERT: A 907 LYS cc_start: 0.8567 (mttt) cc_final: 0.8168 (mtmm) outliers start: 17 outliers final: 13 residues processed: 93 average time/residue: 0.0700 time to fit residues: 8.6123 Evaluate side-chains 88 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.1980 chunk 1 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.151969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128984 restraints weight = 6512.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132194 restraints weight = 4644.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133246 restraints weight = 3827.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134087 restraints weight = 2914.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134300 restraints weight = 2715.971| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5762 Z= 0.105 Angle : 0.515 7.275 7872 Z= 0.261 Chirality : 0.038 0.151 893 Planarity : 0.003 0.036 924 Dihedral : 6.595 88.715 935 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.63 % Allowed : 19.26 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.36), residues: 627 helix: 1.96 (0.31), residues: 294 sheet: -2.90 (0.64), residues: 67 loop : -2.13 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 602 TYR 0.015 0.001 TYR A 390 PHE 0.007 0.001 PHE A 295 TRP 0.007 0.001 TRP A 646 HIS 0.003 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 5758) covalent geometry : angle 0.51533 / 0.26 ( 7872) hydrogen bonds : bond 0.03530 / 2.28 ( 260) hydrogen bonds : angle 3.57817 / 2.49 ( 737) metal coordination : bond 0.00121 / 0.06 ( 3) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8884 (tppt) cc_final: 0.8507 (mmtt) REVERT: A 298 ASN cc_start: 0.8057 (t0) cc_final: 0.7776 (t0) REVERT: A 511 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 529 ASP cc_start: 0.8026 (t0) cc_final: 0.7631 (t0) REVERT: A 907 LYS cc_start: 0.8551 (mttt) cc_final: 0.8211 (mtmm) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.0732 time to fit residues: 9.5186 Evaluate side-chains 90 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 0.0050 overall best weight: 0.5252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.153986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130107 restraints weight = 6552.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.133732 restraints weight = 4467.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134831 restraints weight = 3702.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135805 restraints weight = 2808.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.136987 restraints weight = 2497.794| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5762 Z= 0.105 Angle : 0.524 7.300 7872 Z= 0.263 Chirality : 0.038 0.130 893 Planarity : 0.003 0.036 924 Dihedral : 6.507 88.316 935 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.98 % Allowed : 19.26 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.36), residues: 627 helix: 1.99 (0.31), residues: 294 sheet: -2.87 (0.61), residues: 73 loop : -2.00 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.013 0.001 TYR A 622 PHE 0.007 0.001 PHE A 295 TRP 0.006 0.001 TRP A 646 HIS 0.003 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 5758) covalent geometry : angle 0.52356 / 0.26 ( 7872) hydrogen bonds : bond 0.03482 / 2.27 ( 260) hydrogen bonds : angle 3.53690 / 2.46 ( 737) metal coordination : bond 0.00156 / 0.08 ( 3) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.8906 (tppt) cc_final: 0.8524 (mmtt) REVERT: A 298 ASN cc_start: 0.7887 (t0) cc_final: 0.7556 (t0) REVERT: A 511 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7647 (tm-30) REVERT: A 529 ASP cc_start: 0.8005 (t0) cc_final: 0.7621 (t0) REVERT: A 907 LYS cc_start: 0.8526 (mttt) cc_final: 0.8173 (mtmm) outliers start: 17 outliers final: 15 residues processed: 95 average time/residue: 0.0752 time to fit residues: 9.5067 Evaluate side-chains 95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131629 restraints weight = 6513.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135346 restraints weight = 4534.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.136597 restraints weight = 3716.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.136706 restraints weight = 2789.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137034 restraints weight = 2766.021| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5762 Z= 0.126 Angle : 0.546 7.599 7872 Z= 0.276 Chirality : 0.038 0.162 893 Planarity : 0.003 0.035 924 Dihedral : 6.542 88.103 935 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.80 % Allowed : 19.61 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.36), residues: 627 helix: 1.98 (0.31), residues: 294 sheet: -2.78 (0.69), residues: 61 loop : -2.01 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 811 TYR 0.015 0.001 TYR A 390 PHE 0.009 0.001 PHE A 295 TRP 0.006 0.001 TRP A 512 HIS 0.003 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 5758) covalent geometry : angle 0.54647 / 0.28 ( 7872) hydrogen bonds : bond 0.03636 / 2.39 ( 260) hydrogen bonds : angle 3.59140 / 2.50 ( 737) metal coordination : bond 0.00183 / 0.10 ( 3) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ASN cc_start: 0.7886 (t0) cc_final: 0.7542 (t0) REVERT: A 511 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7701 (tm-30) REVERT: A 529 ASP cc_start: 0.7989 (t0) cc_final: 0.7562 (t0) REVERT: A 907 LYS cc_start: 0.8540 (mttt) cc_final: 0.8193 (mtmm) outliers start: 16 outliers final: 14 residues processed: 94 average time/residue: 0.0712 time to fit residues: 8.9879 Evaluate side-chains 91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116953 restraints weight = 7026.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120308 restraints weight = 4403.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121521 restraints weight = 3343.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122067 restraints weight = 2691.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122655 restraints weight = 2545.734| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5762 Z= 0.114 Angle : 0.567 8.232 7872 Z= 0.285 Chirality : 0.038 0.158 893 Planarity : 0.003 0.035 924 Dihedral : 6.488 87.721 935 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.15 % Allowed : 20.32 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.36), residues: 627 helix: 2.08 (0.31), residues: 293 sheet: -2.93 (0.67), residues: 63 loop : -1.97 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 811 TYR 0.014 0.001 TYR A 622 PHE 0.007 0.001 PHE A 460 TRP 0.006 0.001 TRP A 512 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 5758) covalent geometry : angle 0.56717 / 0.28 ( 7872) hydrogen bonds : bond 0.03531 / 2.31 ( 260) hydrogen bonds : angle 3.55171 / 2.47 ( 737) metal coordination : bond 0.00094 / 0.05 ( 3) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ASN cc_start: 0.7891 (t0) cc_final: 0.7501 (t0) REVERT: A 511 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 907 LYS cc_start: 0.8528 (mttt) cc_final: 0.8132 (mtmm) outliers start: 18 outliers final: 16 residues processed: 91 average time/residue: 0.0776 time to fit residues: 9.3168 Evaluate side-chains 96 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 8 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117774 restraints weight = 7190.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121287 restraints weight = 4468.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122473 restraints weight = 3350.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123273 restraints weight = 2675.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123527 restraints weight = 2496.941| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5762 Z= 0.111 Angle : 0.554 7.259 7872 Z= 0.282 Chirality : 0.038 0.155 893 Planarity : 0.003 0.036 924 Dihedral : 6.431 87.487 935 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.63 % Allowed : 20.84 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.36), residues: 627 helix: 2.13 (0.31), residues: 294 sheet: -2.83 (0.62), residues: 73 loop : -1.94 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.014 0.001 TYR A 390 PHE 0.007 0.001 PHE A 460 TRP 0.006 0.001 TRP A 512 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 5758) covalent geometry : angle 0.55421 / 0.28 ( 7872) hydrogen bonds : bond 0.03401 / 2.21 ( 260) hydrogen bonds : angle 3.55033 / 2.49 ( 737) metal coordination : bond 0.00116 / 0.06 ( 3) Misc. bond : bond 0.00011 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ASN cc_start: 0.7890 (t0) cc_final: 0.7520 (t0) REVERT: A 434 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8534 (tt) REVERT: A 511 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 541 TYR cc_start: 0.8102 (m-80) cc_final: 0.7781 (m-80) REVERT: A 556 GLU cc_start: 0.7370 (tt0) cc_final: 0.7122 (mt-10) REVERT: A 588 GLN cc_start: 0.7474 (pp30) cc_final: 0.7200 (pp30) REVERT: A 907 LYS cc_start: 0.8593 (mttt) cc_final: 0.8127 (mtmm) outliers start: 15 outliers final: 12 residues processed: 96 average time/residue: 0.0663 time to fit residues: 8.5369 Evaluate side-chains 93 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 771 TRP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 0.0970 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116505 restraints weight = 7097.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120081 restraints weight = 4483.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121361 restraints weight = 3340.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121888 restraints weight = 2658.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122047 restraints weight = 2572.891| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5762 Z= 0.116 Angle : 0.562 7.448 7872 Z= 0.284 Chirality : 0.039 0.180 893 Planarity : 0.003 0.043 924 Dihedral : 6.439 87.296 935 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.63 % Allowed : 20.67 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.36), residues: 627 helix: 2.08 (0.31), residues: 294 sheet: -2.95 (0.56), residues: 86 loop : -1.95 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 811 TYR 0.013 0.001 TYR A 390 PHE 0.007 0.001 PHE A 460 TRP 0.007 0.001 TRP A 512 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 5758) covalent geometry : angle 0.56231 / 0.28 ( 7872) hydrogen bonds : bond 0.03536 / 2.33 ( 260) hydrogen bonds : angle 3.56818 / 2.51 ( 737) metal coordination : bond 0.00081 / 0.04 ( 3) Misc. bond : bond 0.00011 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 989.70 seconds wall clock time: 17 minutes 54.47 seconds (1074.47 seconds total)