Starting phenix.real_space_refine on Wed Feb 4 16:13:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgi_53131/02_2026/9qgi_53131_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgi_53131/02_2026/9qgi_53131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qgi_53131/02_2026/9qgi_53131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgi_53131/02_2026/9qgi_53131.map" model { file = "/net/cci-nas-00/data/ceres_data/9qgi_53131/02_2026/9qgi_53131_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgi_53131/02_2026/9qgi_53131_neut.cif" } resolution = 3.16 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= 0.019 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 51 5.16 5 C 7185 2.51 5 N 1934 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11311 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2423 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 275} Chain: "B" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7661 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 48, 'TRANS': 925} Chain breaks: 1 Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.94, per 1000 atoms: 0.26 Number of scatterers: 11311 At special positions: 0 Unit cell: (96.28, 97.94, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 1 15.00 O 2140 8.00 N 1934 7.00 C 7185 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: 0.95 Conformation dependent library (CDL) restraints added in 643.9 milliseconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2682 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 12 sheets defined 47.3% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 4582 through 4593 removed outlier: 4.487A pdb=" N LYS A4593 " --> pdb=" O GLU A4589 " (cutoff:3.500A) Processing helix chain 'A' and resid 4618 through 4626 Processing helix chain 'A' and resid 4630 through 4648 removed outlier: 4.164A pdb=" N VAL A4634 " --> pdb=" O HIS A4630 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS A4635 " --> pdb=" O PRO A4631 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A4646 " --> pdb=" O VAL A4642 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A4648 " --> pdb=" O LEU A4644 " (cutoff:3.500A) Processing helix chain 'A' and resid 4726 through 4730 Processing helix chain 'A' and resid 4746 through 4758 Processing helix chain 'A' and resid 4762 through 4767 removed outlier: 3.731A pdb=" N GLU A4767 " --> pdb=" O TYR A4764 " (cutoff:3.500A) Processing helix chain 'A' and resid 4769 through 4774 removed outlier: 3.772A pdb=" N ARG A4772 " --> pdb=" O GLY A4769 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A4774 " --> pdb=" O GLU A4771 " (cutoff:3.500A) Processing helix chain 'A' and resid 4776 through 4798 removed outlier: 3.501A pdb=" N GLN A4792 " --> pdb=" O SER A4788 " (cutoff:3.500A) Processing helix chain 'A' and resid 4799 through 4805 Processing helix chain 'A' and resid 4810 through 4821 Processing helix chain 'A' and resid 4821 through 4837 Processing helix chain 'A' and resid 4842 through 4868 removed outlier: 3.771A pdb=" N THR A4848 " --> pdb=" O ARG A4844 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS A4862 " --> pdb=" O ARG A4858 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 6.965A pdb=" N ARG B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.538A pdb=" N SER B 259 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 271 through 282 removed outlier: 4.242A pdb=" N ALA B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 469 through 488 removed outlier: 3.629A pdb=" N THR B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 512 Processing helix chain 'B' and resid 517 through 528 Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.545A pdb=" N ASP B 536 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 570 Processing helix chain 'B' and resid 576 through 581 removed outlier: 3.647A pdb=" N GLN B 581 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 3.934A pdb=" N ILE B 593 " --> pdb=" O SER B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 604 Processing helix chain 'B' and resid 613 through 627 Processing helix chain 'B' and resid 644 through 650 removed outlier: 3.664A pdb=" N ASN B 649 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 650 " --> pdb=" O ASN B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.792A pdb=" N VAL B 659 " --> pdb=" O PRO B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 675 Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.860A pdb=" N GLU B 692 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.767A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 removed outlier: 3.661A pdb=" N ARG B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 771 Processing helix chain 'B' and resid 775 through 792 Processing helix chain 'B' and resid 795 through 804 Processing helix chain 'B' and resid 806 through 812 Processing helix chain 'B' and resid 817 through 831 removed outlier: 3.607A pdb=" N SER B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 854 Processing helix chain 'B' and resid 854 through 864 Processing helix chain 'B' and resid 893 through 912 Processing helix chain 'B' and resid 918 through 927 removed outlier: 3.525A pdb=" N GLN B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 976 Processing helix chain 'B' and resid 996 through 1012 Processing helix chain 'B' and resid 1018 through 1027 Processing helix chain 'B' and resid 1033 through 1054 removed outlier: 3.548A pdb=" N THR B1037 " --> pdb=" O ILE B1033 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B1054 " --> pdb=" O LYS B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1116 Processing helix chain 'B' and resid 1136 through 1144 Processing helix chain 'B' and resid 1147 through 1157 Processing helix chain 'C' and resid 22 through 35 removed outlier: 4.238A pdb=" N LYS C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'E' and resid 22 through 34 Processing helix chain 'E' and resid 37 through 41 Processing sheet with id=AA1, first strand: chain 'A' and resid 4596 through 4599 removed outlier: 6.650A pdb=" N ILE A4667 " --> pdb=" O ASP A4661 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4602 through 4604 Processing sheet with id=AA3, first strand: chain 'B' and resid 288 through 292 removed outlier: 6.762A pdb=" N ILE B 220 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N HIS B 247 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LEU B 222 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 219 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL B 308 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 221 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N THR B 310 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER B 223 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR B 563 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 353 Processing sheet with id=AA5, first strand: chain 'B' and resid 410 through 411 removed outlier: 4.590A pdb=" N TYR B 392 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL B 398 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY B 434 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY B 435 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B 378 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE B 369 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL B 376 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 375 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 680 through 683 removed outlier: 6.268A pdb=" N ILE B 635 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR B 683 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 637 " --> pdb=" O TYR B 683 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS B 606 " --> pdb=" O GLY B 705 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N ALA B 707 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 608 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR B 733 " --> pdb=" O ASN B 708 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1084 through 1086 Processing sheet with id=AA8, first strand: chain 'B' and resid 1097 through 1099 removed outlier: 6.318A pdb=" N PHE B1097 " --> pdb=" O ARG B1187 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR B1189 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B1099 " --> pdb=" O THR B1189 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU B1170 " --> pdb=" O LEU B1123 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B1123 " --> pdb=" O GLU B1170 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS B1172 " --> pdb=" O THR B1121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1097 through 1099 removed outlier: 6.318A pdb=" N PHE B1097 " --> pdb=" O ARG B1187 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR B1189 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B1099 " --> pdb=" O THR B1189 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS B1173 " --> pdb=" O VAL B1181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 15 Processing sheet with id=AB2, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AB3, first strand: chain 'E' and resid 12 through 16 removed outlier: 4.071A pdb=" N ARG E 42 " --> pdb=" O VAL E 70 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1485 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: 2.35 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3741 1.34 - 1.47: 2576 1.47 - 1.59: 5159 1.59 - 1.71: 1 1.71 - 1.83: 76 Bond restraints: 11553 Sorted by residual: bond pdb=" CB CYS B 767 " pdb=" SG CYS B 767 " ideal model delta sigma weight residual 1.808 1.443 0.365 3.30e-02 9.18e+02 1.22e+02 bond pdb=" CA GLY C 75 " pdb=" C GLY C 75 " ideal model delta sigma weight residual 1.512 1.553 -0.041 1.14e-02 7.69e+03 1.28e+01 bond pdb=" CA SER E 20 " pdb=" CB SER E 20 " ideal model delta sigma weight residual 1.539 1.498 0.041 1.20e-02 6.94e+03 1.17e+01 bond pdb=" N GLY C 75 " pdb=" CA GLY C 75 " ideal model delta sigma weight residual 1.449 1.485 -0.036 1.21e-02 6.83e+03 8.91e+00 bond pdb=" CA THR E 22 " pdb=" C THR E 22 " ideal model delta sigma weight residual 1.525 1.486 0.038 1.32e-02 5.74e+03 8.46e+00 ... (remaining 11548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 15342 1.87 - 3.75: 248 3.75 - 5.62: 34 5.62 - 7.49: 11 7.49 - 9.36: 4 Bond angle restraints: 15639 Sorted by residual: angle pdb=" N PRO E 19 " pdb=" CA PRO E 19 " pdb=" C PRO E 19 " ideal model delta sigma weight residual 111.22 104.13 7.09 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CA THR E 22 " pdb=" CB THR E 22 " pdb=" OG1 THR E 22 " ideal model delta sigma weight residual 109.60 102.71 6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" N GLY C 75 " pdb=" CA GLY C 75 " pdb=" C GLY C 75 " ideal model delta sigma weight residual 110.80 116.56 -5.76 1.41e+00 5.03e-01 1.67e+01 angle pdb=" C GLY C 75 " pdb=" N ALA C 76 " pdb=" CA ALA C 76 " ideal model delta sigma weight residual 121.70 128.56 -6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" N GLU E 18 " pdb=" CA GLU E 18 " pdb=" C GLU E 18 " ideal model delta sigma weight residual 110.40 105.49 4.91 1.31e+00 5.83e-01 1.40e+01 ... (remaining 15634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6285 17.99 - 35.98: 581 35.98 - 53.97: 104 53.97 - 71.97: 29 71.97 - 89.96: 18 Dihedral angle restraints: 7017 sinusoidal: 2879 harmonic: 4138 Sorted by residual: dihedral pdb=" CA MET C 1 " pdb=" C MET C 1 " pdb=" N GLN C 2 " pdb=" CA GLN C 2 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLN C 49 " pdb=" C GLN C 49 " pdb=" N LEU C 50 " pdb=" CA LEU C 50 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP B 381 " pdb=" CB ASP B 381 " pdb=" CG ASP B 381 " pdb=" OD1 ASP B 381 " ideal model delta sinusoidal sigma weight residual -30.00 -86.57 56.57 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 7014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1349 0.045 - 0.090: 280 0.090 - 0.136: 102 0.136 - 0.181: 2 0.181 - 0.226: 3 Chirality restraints: 1736 Sorted by residual: chirality pdb=" C3' AMP E 101 " pdb=" C2' AMP E 101 " pdb=" C4' AMP E 101 " pdb=" O3' AMP E 101 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA VAL E 17 " pdb=" N VAL E 17 " pdb=" C VAL E 17 " pdb=" CB VAL E 17 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE E 23 " pdb=" N ILE E 23 " pdb=" C ILE E 23 " pdb=" CB ILE E 23 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 1733 not shown) Planarity restraints: 2037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A4719 " 0.048 2.00e-02 2.50e+03 2.63e-02 1.39e+01 pdb=" CG TYR A4719 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A4719 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A4719 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A4719 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A4719 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A4719 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A4719 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 68 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C HIS C 68 " 0.041 2.00e-02 2.50e+03 pdb=" O HIS C 68 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU C 69 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 16 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C GLU E 16 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU E 16 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL E 17 " 0.013 2.00e-02 2.50e+03 ... (remaining 2034 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.76: 1758 2.76 - 3.48: 15832 3.48 - 4.19: 26828 4.19 - 4.90: 48750 Nonbonded interactions: 93170 Sorted by model distance: nonbonded pdb=" SG CYS B 767 " pdb=" C ALA C 76 " model vdw 1.340 3.630 nonbonded pdb=" SG CYS A4725 " pdb=" CB ALA C 76 " model vdw 1.830 3.820 nonbonded pdb=" SG CYS B 767 " pdb=" O ALA C 76 " model vdw 2.213 3.400 nonbonded pdb=" O LEU B 710 " pdb=" CB ALA E 76 " model vdw 2.240 3.460 nonbonded pdb=" N PRO E 19 " pdb=" O PRO E 19 " model vdw 2.460 2.496 ... (remaining 93165 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) } 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: 4.070 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.050 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 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 0.365 11554 Z= 0.185 Angle : 0.584 9.363 15639 Z= 0.321 Chirality : 0.042 0.226 1736 Planarity : 0.004 0.036 2037 Dihedral : 15.071 89.958 4335 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.80 % Allowed : 11.97 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.71 (0.23), residues: 1412 helix: 1.92 (0.22), residues: 577 sheet: 0.97 (0.35), residues: 250 loop : 0.53 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 42 TYR 0.048 0.001 TYR A4719 PHE 0.016 0.001 PHE B 564 TRP 0.008 0.001 TRP A4732 HIS 0.002 0.000 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00444 (11553) covalent geometry : angle 0.58442 (15639) hydrogen bonds : bond 0.14455 ( 536) hydrogen bonds : angle 5.87953 ( 1485) Misc. bond : bond 0.00066 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8804 (tm-30) REVERT: B 401 MET cc_start: 0.8235 (mtt) cc_final: 0.7825 (mtp) REVERT: B 640 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8708 (pmt) REVERT: B 806 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8026 (pp30) REVERT: B 817 ILE cc_start: 0.8656 (pt) cc_final: 0.8378 (mm) REVERT: B 821 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8762 (mt-10) REVERT: B 1148 MET cc_start: 0.8800 (mmm) cc_final: 0.8489 (tpp) REVERT: C 59 TYR cc_start: 0.5065 (OUTLIER) cc_final: 0.3270 (m-10) REVERT: E 34 GLU cc_start: 0.8282 (mp0) cc_final: 0.7963 (mp0) REVERT: E 51 GLU cc_start: 0.9002 (pt0) cc_final: 0.8720 (pm20) REVERT: E 52 ASP cc_start: 0.8733 (m-30) cc_final: 0.8509 (m-30) REVERT: E 55 THR cc_start: 0.9031 (p) cc_final: 0.8512 (t) REVERT: E 74 ARG cc_start: 0.7909 (ptp-110) cc_final: 0.7402 (mtm180) outliers start: 10 outliers final: 5 residues processed: 104 average time/residue: 0.1113 time to fit residues: 17.1359 Evaluate side-chains 95 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4694 ASP Chi-restraints excluded: chain A residue 4727 SER Chi-restraints excluded: chain A residue 4813 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4639 GLN A4840 GLN B 647 ASN E 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053180 restraints weight = 33016.692| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.45 r_work: 0.2710 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11554 Z= 0.234 Angle : 0.570 7.431 15639 Z= 0.291 Chirality : 0.043 0.162 1736 Planarity : 0.004 0.039 2037 Dihedral : 5.141 50.758 1555 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.29 % Allowed : 11.33 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.70 (0.23), residues: 1412 helix: 2.02 (0.22), residues: 583 sheet: 0.82 (0.35), residues: 236 loop : 0.47 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 42 TYR 0.018 0.001 TYR B 901 PHE 0.012 0.001 PHE B 555 TRP 0.008 0.001 TRP B 607 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00541 (11553) covalent geometry : angle 0.57045 (15639) hydrogen bonds : bond 0.04204 ( 536) hydrogen bonds : angle 4.65567 ( 1485) Misc. bond : bond 0.00167 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 401 MET cc_start: 0.8285 (mtt) cc_final: 0.7910 (mtp) REVERT: B 640 MET cc_start: 0.9347 (pmt) cc_final: 0.8763 (pmt) REVERT: B 806 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8124 (pp30) REVERT: B 817 ILE cc_start: 0.8680 (pt) cc_final: 0.8440 (mm) REVERT: B 821 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8843 (mt-10) REVERT: C 59 TYR cc_start: 0.5206 (OUTLIER) cc_final: 0.3251 (m-10) REVERT: E 51 GLU cc_start: 0.8970 (pt0) cc_final: 0.8628 (pm20) REVERT: E 62 GLN cc_start: 0.9296 (mt0) cc_final: 0.8898 (mm110) REVERT: E 63 LYS cc_start: 0.9423 (mtpp) cc_final: 0.8075 (mmmm) outliers start: 16 outliers final: 7 residues processed: 97 average time/residue: 0.1057 time to fit residues: 15.5565 Evaluate side-chains 84 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4813 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 647 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.074931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.054797 restraints weight = 33180.454| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.56 r_work: 0.2729 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11554 Z= 0.113 Angle : 0.498 8.261 15639 Z= 0.255 Chirality : 0.041 0.152 1736 Planarity : 0.003 0.039 2037 Dihedral : 4.757 51.725 1548 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.64 % Allowed : 11.89 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.78 (0.23), residues: 1412 helix: 2.09 (0.22), residues: 583 sheet: 0.92 (0.35), residues: 228 loop : 0.48 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.015 0.001 TYR B 901 PHE 0.013 0.001 PHE B1108 TRP 0.005 0.001 TRP B 607 HIS 0.002 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00251 (11553) covalent geometry : angle 0.49818 (15639) hydrogen bonds : bond 0.03461 ( 536) hydrogen bonds : angle 4.41890 ( 1485) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4628 ARG cc_start: 0.9091 (mtt90) cc_final: 0.8604 (mtp180) REVERT: B 401 MET cc_start: 0.8213 (mtt) cc_final: 0.7992 (mtp) REVERT: B 640 MET cc_start: 0.9328 (pmt) cc_final: 0.8747 (pmt) REVERT: B 732 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 806 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8199 (pp30) REVERT: B 817 ILE cc_start: 0.8560 (pt) cc_final: 0.8295 (mm) REVERT: B 821 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8820 (mt-10) REVERT: C 59 TYR cc_start: 0.5340 (OUTLIER) cc_final: 0.3377 (m-10) REVERT: E 24 GLU cc_start: 0.8498 (mp0) cc_final: 0.8149 (mp0) REVERT: E 51 GLU cc_start: 0.8980 (pt0) cc_final: 0.8585 (pm20) REVERT: E 62 GLN cc_start: 0.9147 (mt0) cc_final: 0.8799 (mm110) REVERT: E 74 ARG cc_start: 0.7989 (ptp-110) cc_final: 0.7577 (mtm-85) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.1116 time to fit residues: 15.7591 Evaluate side-chains 84 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4813 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 chunk 125 optimal weight: 0.0070 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 overall best weight: 0.5400 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.075245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.055059 restraints weight = 33008.116| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.56 r_work: 0.2750 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11554 Z= 0.094 Angle : 0.476 6.854 15639 Z= 0.242 Chirality : 0.040 0.153 1736 Planarity : 0.003 0.038 2037 Dihedral : 4.573 51.743 1548 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.80 % Allowed : 12.21 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1412 helix: 2.16 (0.22), residues: 584 sheet: 1.16 (0.36), residues: 223 loop : 0.51 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.014 0.001 TYR B 901 PHE 0.013 0.001 PHE B1108 TRP 0.005 0.001 TRP B 607 HIS 0.002 0.000 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00205 (11553) covalent geometry : angle 0.47604 (15639) hydrogen bonds : bond 0.03061 ( 536) hydrogen bonds : angle 4.23686 ( 1485) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: B 640 MET cc_start: 0.9346 (pmt) cc_final: 0.8716 (pmt) REVERT: B 732 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8387 (tm-30) REVERT: B 806 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8218 (pp30) REVERT: B 817 ILE cc_start: 0.8532 (pt) cc_final: 0.8231 (mm) REVERT: B 821 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8806 (mt-10) REVERT: C 59 TYR cc_start: 0.5371 (OUTLIER) cc_final: 0.3414 (m-10) REVERT: E 21 ASP cc_start: 0.8112 (p0) cc_final: 0.7895 (p0) REVERT: E 24 GLU cc_start: 0.8572 (mp0) cc_final: 0.8218 (mp0) REVERT: E 51 GLU cc_start: 0.8985 (pt0) cc_final: 0.8569 (pm20) REVERT: E 55 THR cc_start: 0.9176 (p) cc_final: 0.8621 (t) REVERT: E 62 GLN cc_start: 0.9275 (mt0) cc_final: 0.8834 (mm110) REVERT: E 63 LYS cc_start: 0.9465 (mtpp) cc_final: 0.8478 (mmmm) REVERT: E 74 ARG cc_start: 0.7910 (ptp-110) cc_final: 0.7543 (mtm-85) outliers start: 10 outliers final: 5 residues processed: 90 average time/residue: 0.1083 time to fit residues: 14.8389 Evaluate side-chains 87 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4813 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 51 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 25 optimal weight: 0.0000 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.7390 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.072913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.053039 restraints weight = 33032.915| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.44 r_work: 0.2714 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11554 Z= 0.173 Angle : 0.506 6.651 15639 Z= 0.257 Chirality : 0.041 0.146 1736 Planarity : 0.003 0.039 2037 Dihedral : 4.588 51.653 1548 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.04 % Allowed : 12.29 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.83 (0.23), residues: 1412 helix: 2.20 (0.22), residues: 584 sheet: 0.91 (0.35), residues: 231 loop : 0.44 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4594 TYR 0.016 0.001 TYR B 901 PHE 0.016 0.001 PHE B1108 TRP 0.007 0.001 TRP A4732 HIS 0.002 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00403 (11553) covalent geometry : angle 0.50573 (15639) hydrogen bonds : bond 0.03456 ( 536) hydrogen bonds : angle 4.25680 ( 1485) Misc. bond : bond 0.00088 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 303 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9153 (mtmm) REVERT: B 640 MET cc_start: 0.9386 (pmt) cc_final: 0.8782 (pmt) REVERT: B 806 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8274 (pp30) REVERT: B 817 ILE cc_start: 0.8622 (pt) cc_final: 0.8372 (mm) REVERT: B 821 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8863 (mt-10) REVERT: E 24 GLU cc_start: 0.8565 (mp0) cc_final: 0.8290 (mp0) REVERT: E 51 GLU cc_start: 0.8930 (pt0) cc_final: 0.8611 (pm20) REVERT: E 55 THR cc_start: 0.9248 (p) cc_final: 0.8757 (t) REVERT: E 62 GLN cc_start: 0.9112 (mt0) cc_final: 0.8777 (mm110) REVERT: E 74 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7677 (mtm-85) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.1041 time to fit residues: 14.3707 Evaluate side-chains 91 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4732 TRP Chi-restraints excluded: chain A residue 4794 CYS Chi-restraints excluded: chain A residue 4813 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 86 optimal weight: 0.0030 chunk 61 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.074791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054631 restraints weight = 33204.033| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.55 r_work: 0.2740 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11554 Z= 0.097 Angle : 0.474 6.612 15639 Z= 0.241 Chirality : 0.040 0.152 1736 Planarity : 0.003 0.038 2037 Dihedral : 4.461 51.285 1548 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.29 % Allowed : 12.77 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.87 (0.23), residues: 1412 helix: 2.23 (0.22), residues: 585 sheet: 0.88 (0.37), residues: 214 loop : 0.50 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4628 TYR 0.014 0.001 TYR B 901 PHE 0.018 0.001 PHE B1108 TRP 0.006 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00216 (11553) covalent geometry : angle 0.47450 (15639) hydrogen bonds : bond 0.03010 ( 536) hydrogen bonds : angle 4.14799 ( 1485) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 640 MET cc_start: 0.9363 (pmt) cc_final: 0.8672 (pmt) REVERT: B 732 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 806 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8220 (pp30) REVERT: B 817 ILE cc_start: 0.8546 (pt) cc_final: 0.8259 (mm) REVERT: B 821 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8809 (mt-10) REVERT: E 2 GLN cc_start: 0.9176 (tt0) cc_final: 0.8947 (tt0) REVERT: E 24 GLU cc_start: 0.8583 (mp0) cc_final: 0.8265 (mp0) REVERT: E 29 LYS cc_start: 0.9389 (mttp) cc_final: 0.9185 (mtmt) REVERT: E 34 GLU cc_start: 0.7978 (mp0) cc_final: 0.7649 (mp0) REVERT: E 51 GLU cc_start: 0.8959 (pt0) cc_final: 0.8546 (pm20) REVERT: E 55 THR cc_start: 0.9216 (p) cc_final: 0.8683 (t) REVERT: E 62 GLN cc_start: 0.9178 (mt0) cc_final: 0.8823 (mm110) REVERT: E 63 LYS cc_start: 0.9295 (mmmt) cc_final: 0.8974 (mmmm) outliers start: 16 outliers final: 10 residues processed: 95 average time/residue: 0.1029 time to fit residues: 14.8781 Evaluate side-chains 91 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4732 TRP Chi-restraints excluded: chain A residue 4794 CYS Chi-restraints excluded: chain A residue 4813 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 56 optimal weight: 0.0770 chunk 116 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 1.4142 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.073708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053702 restraints weight = 33149.070| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.46 r_work: 0.2718 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11554 Z= 0.146 Angle : 0.497 8.080 15639 Z= 0.250 Chirality : 0.041 0.163 1736 Planarity : 0.003 0.039 2037 Dihedral : 4.441 51.195 1548 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.29 % Allowed : 12.77 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.87 (0.23), residues: 1412 helix: 2.28 (0.22), residues: 584 sheet: 0.84 (0.37), residues: 217 loop : 0.46 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 74 TYR 0.015 0.001 TYR B 901 PHE 0.016 0.001 PHE B1108 TRP 0.007 0.001 TRP B 782 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00339 (11553) covalent geometry : angle 0.49720 (15639) hydrogen bonds : bond 0.03265 ( 536) hydrogen bonds : angle 4.19384 ( 1485) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: B 303 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9131 (mtmm) REVERT: B 640 MET cc_start: 0.9385 (pmt) cc_final: 0.8714 (pmt) REVERT: B 732 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8303 (tm-30) REVERT: B 741 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8879 (p0) REVERT: B 806 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8228 (pp30) REVERT: B 817 ILE cc_start: 0.8610 (pt) cc_final: 0.8325 (mm) REVERT: B 821 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8789 (mt-10) REVERT: E 24 GLU cc_start: 0.8566 (mp0) cc_final: 0.8271 (mp0) REVERT: E 55 THR cc_start: 0.9252 (p) cc_final: 0.8770 (t) REVERT: E 62 GLN cc_start: 0.9164 (mt0) cc_final: 0.8846 (mm110) REVERT: E 74 ARG cc_start: 0.8048 (ptp-110) cc_final: 0.7660 (mtm-85) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 0.1117 time to fit residues: 15.6911 Evaluate side-chains 91 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4732 TRP Chi-restraints excluded: chain A residue 4813 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 101 optimal weight: 0.9980 overall best weight: 0.7738 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.074298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.054166 restraints weight = 32777.873| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.45 r_work: 0.2736 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11554 Z= 0.102 Angle : 0.476 7.791 15639 Z= 0.240 Chirality : 0.040 0.161 1736 Planarity : 0.003 0.040 2037 Dihedral : 4.381 51.215 1548 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.04 % Allowed : 13.01 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1412 helix: 2.26 (0.22), residues: 585 sheet: 0.86 (0.37), residues: 214 loop : 0.53 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 74 TYR 0.014 0.001 TYR B 901 PHE 0.014 0.001 PHE B1108 TRP 0.006 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00229 (11553) covalent geometry : angle 0.47592 (15639) hydrogen bonds : bond 0.03020 ( 536) hydrogen bonds : angle 4.12315 ( 1485) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 4587 TYR cc_start: 0.8908 (t80) cc_final: 0.8590 (t80) REVERT: B 303 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9145 (mtmm) REVERT: B 640 MET cc_start: 0.9384 (pmt) cc_final: 0.8693 (pmt) REVERT: B 732 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8300 (tm-30) REVERT: B 741 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.8837 (p0) REVERT: B 806 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8230 (pp30) REVERT: B 817 ILE cc_start: 0.8568 (pt) cc_final: 0.8275 (mm) REVERT: B 821 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8812 (mt-10) REVERT: E 24 GLU cc_start: 0.8611 (mp0) cc_final: 0.8277 (mp0) REVERT: E 25 ASN cc_start: 0.9376 (m-40) cc_final: 0.8567 (t0) REVERT: E 55 THR cc_start: 0.9259 (p) cc_final: 0.8782 (t) REVERT: E 62 GLN cc_start: 0.9187 (mt0) cc_final: 0.8823 (mm110) REVERT: E 63 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8813 (mmmt) REVERT: E 74 ARG cc_start: 0.8031 (ptp-110) cc_final: 0.7678 (mtm-85) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 0.1090 time to fit residues: 14.9804 Evaluate side-chains 92 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4732 TRP Chi-restraints excluded: chain A residue 4794 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.1980 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.074971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.054927 restraints weight = 32905.160| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.52 r_work: 0.2745 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 11554 Z= 0.098 Angle : 0.490 8.258 15639 Z= 0.247 Chirality : 0.040 0.157 1736 Planarity : 0.003 0.039 2037 Dihedral : 4.217 51.010 1545 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.80 % Allowed : 13.33 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.92 (0.23), residues: 1412 helix: 2.22 (0.22), residues: 586 sheet: 1.03 (0.38), residues: 209 loop : 0.54 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 72 TYR 0.014 0.001 TYR B 901 PHE 0.013 0.001 PHE B1108 TRP 0.006 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00222 (11553) covalent geometry : angle 0.49038 (15639) hydrogen bonds : bond 0.02941 ( 536) hydrogen bonds : angle 4.11566 ( 1485) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 4587 TYR cc_start: 0.8896 (t80) cc_final: 0.8646 (t80) REVERT: B 640 MET cc_start: 0.9340 (pmt) cc_final: 0.8620 (pmt) REVERT: B 732 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 741 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8780 (p0) REVERT: B 806 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8242 (pp30) REVERT: B 817 ILE cc_start: 0.8532 (pt) cc_final: 0.8225 (mm) REVERT: B 821 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8790 (mt-10) REVERT: E 24 GLU cc_start: 0.8632 (mp0) cc_final: 0.8280 (mp0) REVERT: E 25 ASN cc_start: 0.9347 (m-40) cc_final: 0.8550 (t0) REVERT: E 29 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8893 (mtpp) REVERT: E 51 GLU cc_start: 0.8616 (pm20) cc_final: 0.8214 (pm20) REVERT: E 55 THR cc_start: 0.9241 (p) cc_final: 0.8764 (t) REVERT: E 62 GLN cc_start: 0.9232 (mt0) cc_final: 0.8814 (mm110) REVERT: E 74 ARG cc_start: 0.7997 (ptp-110) cc_final: 0.7684 (mtm-85) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.1004 time to fit residues: 13.7595 Evaluate side-chains 94 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4732 TRP Chi-restraints excluded: chain A residue 4794 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.074239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054182 restraints weight = 33228.153| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.54 r_work: 0.2717 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11554 Z= 0.130 Angle : 0.511 9.615 15639 Z= 0.257 Chirality : 0.041 0.171 1736 Planarity : 0.003 0.051 2037 Dihedral : 4.233 50.880 1545 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.80 % Allowed : 13.65 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.83 (0.23), residues: 1412 helix: 2.18 (0.22), residues: 586 sheet: 0.72 (0.37), residues: 221 loop : 0.55 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 72 TYR 0.015 0.001 TYR B 901 PHE 0.014 0.001 PHE B1108 TRP 0.005 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00303 (11553) covalent geometry : angle 0.51084 (15639) hydrogen bonds : bond 0.03129 ( 536) hydrogen bonds : angle 4.14487 ( 1485) Misc. bond : bond 0.00043 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 4587 TYR cc_start: 0.8911 (t80) cc_final: 0.8665 (t80) REVERT: B 640 MET cc_start: 0.9326 (pmt) cc_final: 0.8602 (pmt) REVERT: B 732 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 741 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8791 (p0) REVERT: B 806 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8233 (pp30) REVERT: B 817 ILE cc_start: 0.8547 (pt) cc_final: 0.8240 (mm) REVERT: B 821 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8807 (mt-10) REVERT: E 24 GLU cc_start: 0.8694 (mp0) cc_final: 0.8340 (mp0) REVERT: E 25 ASN cc_start: 0.9361 (m-40) cc_final: 0.8679 (t0) REVERT: E 51 GLU cc_start: 0.8614 (pm20) cc_final: 0.8206 (pm20) REVERT: E 55 THR cc_start: 0.9250 (p) cc_final: 0.8781 (t) REVERT: E 62 GLN cc_start: 0.9213 (mt0) cc_final: 0.8732 (mm110) REVERT: E 74 ARG cc_start: 0.8042 (ptp-110) cc_final: 0.7737 (mtm-85) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 0.1015 time to fit residues: 14.2627 Evaluate side-chains 88 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4732 TRP Chi-restraints excluded: chain A residue 4794 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 741 ASN Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.074457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054431 restraints weight = 32973.653| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.45 r_work: 0.2740 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11554 Z= 0.106 Angle : 0.502 10.503 15639 Z= 0.251 Chirality : 0.041 0.164 1736 Planarity : 0.003 0.039 2037 Dihedral : 4.208 50.832 1545 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.80 % Allowed : 13.57 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.83 (0.23), residues: 1412 helix: 2.18 (0.22), residues: 585 sheet: 0.70 (0.36), residues: 221 loop : 0.56 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 72 TYR 0.014 0.001 TYR B 901 PHE 0.013 0.001 PHE B1108 TRP 0.006 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00245 (11553) covalent geometry : angle 0.50229 (15639) hydrogen bonds : bond 0.02988 ( 536) hydrogen bonds : angle 4.12713 ( 1485) Misc. bond : bond 0.00034 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.80 seconds wall clock time: 43 minutes 11.18 seconds (2591.18 seconds total)